diff --git a/.gitignore b/.gitignore
index 2faeee7..7aff408 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@
 
 /logs/
 
+.idea/*
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f5c7e53..5f0f429 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,7 +1,25 @@
 # Change Log
+
 All notable changes to this project will be documented in this file.
 See the [change log guidelines](http://keepachangelog.com/) for information on how to structure the file.
 
+## [5.1.0]
+
+### Added
+
+- Upgrade hale dependencies to 5.1 and Java version to 17.
+- Added support for specifying filters when loading data.
+
+### Changed
+
+- Always use the latest versions of hale offline resources like INSPIRE schemas.
+- Include support for MS Access.
+
+### Fixed
+
+- Fixed a problem that lead to alignment migration failing if collection of statistics was not enabled.
+- Fixed error when collecting merge statistics for an alignment with custom functions.
+
 ## [4.0.0]
 
 ## Added
@@ -111,6 +129,7 @@ Initial release based on hale studio 3.0.0.
 - Command to generate JSON representations of hale alignments (`hale project alignment export-json`)
 - Experimental command to filter to create a copy of a hale project with a filtered alignment (`hale project alignment filter`)
 
+[5.1.0]: https://github.com/halestudio/hale-cli/compare/v4.0.0...v5.1.0
 [4.0.0]: https://github.com/halestudio/hale-cli/compare/v3.5.0...v4.0.0
 [3.5.0]: https://github.com/halestudio/hale-cli/compare/v3.4.0...v3.5.0
 [3.4.0]: https://github.com/halestudio/hale-cli/compare/v3.3.2...v3.4.0
diff --git a/README.md b/README.md
index 9473662..24d245e 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ Build docker image:
 Run
 ---
 
-You can run the application using Gradle. However, there is no possibility to easily provide arguments.
+You can run the application using Gradle.
 
 ```
 ./gradlew run
@@ -45,6 +45,12 @@ Alternatively, you can run the start script of the built application.
 hale --version
 ```
 
+You can provide arguments to run as string in `""` following the below syntax.
+For example pass argument `help` to run command as below
+```
+./gradlew run --args="help"
+```
+
 If using `./gradlew installDist`, the start script can be found in `./build/install/hale/bin/`.
 
 JVM parameters can be provided to the start script with the `HALE_OPTS` environment variable.
diff --git a/build.gradle b/build.gradle
index c4d2f1d..e6eb7fe 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,33 +1,36 @@
 buildscript {
   repositories {
-    jcenter()
+    mavenCentral()
   }
   dependencies {
-    classpath 'org.standardout:gradle-eclipseconfig:1.0.0'
+    classpath 'org.standardout:gradle-eclipseconfig:1.1.1'
   }
 }
 
 plugins {
   id 'groovy'
   id 'application'
-  id 'maven'
-  id 'osgi'
-  id 'com.bmuschko.docker-java-application' version '3.6.2'
-  id "nebula.ospackage-application" version "3.6.1"
+  id 'maven-publish'
+  //id 'osgi' // discontinued - do we need it?
+  id 'com.bmuschko.docker-java-application' version '9.3.1'
+  id "nebula.ospackage-application" version "9.1.1"
   id 'org.ajoberstar.grgit' version '1.5.0'
 }
 
 apply plugin: 'org.standardout.eclipseconfig'
 
-sourceCompatibility = '1.8'
+// update to java 17
+sourceCompatibility = JavaVersion.VERSION_17
+targetCompatibility = JavaVersion.VERSION_17
 
 group = 'to.wetransform'
 
 project.ext {
-  haleVersion = '4.0.0'
+  haleVersion = '5.1.0'
+  groovyVersion = '2.5.19'
 }
 
-version = '4.0.1-SNAPSHOT'
+version = '5.1.0'
 
 /*
  * Dependencies
@@ -36,11 +39,13 @@ version = '4.0.1-SNAPSHOT'
 repositories {
   // mavenLocal() //XXX for testing
 
+  // merge both snapshot and release repositories to virtual repository named local
+  // because gradle was reporting error if it encountered dependencies from snapshots
+  // but libs-release-local was placed before snapshots here in the hierarchy and also
+  // vice-versa case when dependencies were encountered from release but snapshots
+  // was placed before release
   maven { // wetransform release repository (HALE releases and Eclipse dependencies)
-    url 'https://artifactory.wetransform.to/artifactory/libs-release-local'
-  }
-  maven { // wetransform snapshot repository (HALE snapshots)
-    url 'https://artifactory.wetransform.to/artifactory/libs-snapshot-local'
+    url 'https://artifactory.wetransform.to/artifactory/local'
   }
 
   // this needs to be defined before jcenter/MavenCentral for retrieving JAI
@@ -48,140 +53,137 @@ repositories {
     url 'https://repo.osgeo.org/repository/release/'
   }
 
-  maven { // HALE artifactory (dependencies for HALE)
-    url 'https://artifactory.wetransform.to/artifactory/ext-release-local'
-  }
-
-  jcenter()
+  mavenCentral()
 }
 
 configurations {
   // exclude Saxon9 custom dependency by schema-utils (schematron validation)
-  compile.exclude group: 'org.opengis.cite.saxon', module: 'saxon9'
+  implementation.exclude group: 'org.opengis.cite.saxon', module: 'saxon9'
 }
 
 dependencies {
   // HALE
 
   // CLI API, utilities and default commands
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.util.cli:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.cli:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.app.cli.commands:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.util.cli:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.cli:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.app.cli.commands:$haleVersion"
+
+  implementation "org.codehaus.groovy:groovy-all:$groovyVersion"
 
   // core
-  compile 'eu.esdihumboldt.unpuzzled:org.eclipse.equinox.nonosgi.registry:1.0.0'
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.core:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.align.groovy:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.align.merge:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.referencing:$haleVersion"
+  implementation 'eu.esdihumboldt.unpuzzled:org.eclipse.equinox.nonosgi.registry:1.0.0'
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.core:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.align.groovy:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.align.merge:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.referencing:$haleVersion"
 
   // transformation
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.app.transform:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.app.transform:$haleVersion"
   // needed to run successfully:
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.headless.orient:$haleVersion" // reiterable transformation sink (for WFS FeatureCollection)
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.propertyaccessor:$haleVersion" // for CQL filters to work
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.headless.orient:$haleVersion" // reiterable transformation sink (for WFS FeatureCollection)
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.propertyaccessor:$haleVersion" // for CQL filters to work
   // transformation functions:
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.core:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.inspire:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.geometric:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.groovy:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.groovy.helpers:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.numeric:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.string:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.custom:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.collector:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.core:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.inspire:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.geometric:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.groovy:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.groovy.helpers:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.numeric:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.string:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.custom:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.cst.functions.collector:$haleVersion"
 
   // formats
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.xml:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.xsd:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.gml:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.shp:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.csv:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.wfs:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.json:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.xls:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.geopackage:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.html.svg:$haleVersion"
-  
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.xml:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.xsd:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.gml:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.shp:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.csv:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.wfs:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.json:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.xls:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.geopackage:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.html.svg:$haleVersion"
+
   // database support
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc.postgresql:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc.mssql:$haleVersion"
-  
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc.postgresql:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc.mssql:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.jdbc.msaccess:$haleVersion"
+
   // hale connect
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.haleconnect:$haleVersion"
-  
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.haleconnect:$haleVersion"
+
   // code list formats
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.codelist.xml:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.codelist.xml:$haleVersion"
 
   // Schematron validation
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.schematron:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.io.schematron:$haleVersion"
   // replacement for omitted Saxon dependency
   // tested w/ schematron validation in https://github.com/wetransform/exp-schematron/tree/exp/saxon-he
-  compile 'net.sf.saxon:Saxon-HE:9.7.0-20'
+  implementation 'net.sf.saxon:Saxon-HE:9.7.0-20'
 
   // converters
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.convert.core:$haleVersion"
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.convert.wkt:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.convert.core:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.common.convert.wkt:$haleVersion"
 
   // Groovy meta extensions
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.util.groovy.meta.extension:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.util.groovy.meta.extension:$haleVersion"
 
   // logging
-  compile(group: 'eu.esdihumboldt.unpuzzled', name: 'de.fhg.igd.slf4jplus.logback.appender', version: '1.2.0.201503311443')
-  compile 'org.slf4j:jul-to-slf4j:1.7.21'
+  implementation(group: 'eu.esdihumboldt.unpuzzled', name: 'de.fhg.igd.slf4jplus.logback.appender', version: '1.2.0.201503311443')
+  implementation 'org.slf4j:jul-to-slf4j:1.7.21'
 
   // resource cache
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource', version: haleVersion)
-  def resourcesVersion = '2018.8.7'
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource', version: haleVersion)
+  def resourcesVersion = '2023.10.28'
   // OpenGIS schemas, INSPIRE schemas, W3C schemas, etc.
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.opengis.net', version: resourcesVersion)
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.inspire', version: resourcesVersion)
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.portele.de', version: resourcesVersion)
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.w3.org', version: resourcesVersion)
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.opengis.net', version: resourcesVersion)
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.inspire', version: resourcesVersion)
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.portele.de', version: resourcesVersion)
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.w3.org', version: resourcesVersion)
   // INSPIRE code lists and feature concepts
-  compile(group: 'eu.esdihumboldt.hale',
+  implementation(group: 'eu.esdihumboldt.hale',
     name: 'eu.esdihumboldt.util.resource.codelists.inspire',
     version: resourcesVersion)
-  compile(group: 'eu.esdihumboldt.hale',
+  implementation(group: 'eu.esdihumboldt.hale',
     name: 'eu.esdihumboldt.util.resource.codelists.inspire.accept-xml',
     version: resourcesVersion)
-  compile(group: 'eu.esdihumboldt.hale',
+  implementation(group: 'eu.esdihumboldt.hale',
     name: 'eu.esdihumboldt.util.resource.featureconcepts.inspire',
     version: resourcesVersion)
-
-  // More resources with different version
-  resourcesVersion = '2020.6.29'
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.adv-online.de', version: resourcesVersion)
-  compile(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.xplanung.de', version: resourcesVersion)
+  // More resources
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.adv-online.de', version: resourcesVersion)
+  implementation(group: 'eu.esdihumboldt.hale', name: 'eu.esdihumboldt.util.resource.schemas.xplanung.de', version: resourcesVersion)
 
   // user / customer specific
-  compile "eu.esdihumboldt.hale:eu.esdihumboldt.hale.adv.merge:$haleVersion"
+  implementation "eu.esdihumboldt.hale:eu.esdihumboldt.hale.adv.merge:$haleVersion"
 
   // CLI
-  compile 'commons-cli:commons-cli:1.3.1'
+  implementation 'commons-cli:commons-cli:1.5.0'
   // Groovy Shell
-  compile 'jline:jline:2.13'
+  implementation 'jline:jline:2.13'
 
   // Testing
-  testCompile 'junit:junit:4.12'
-  testCompile 'com.github.stefanbirkner:system-rules:1.16.0'
+  testImplementation 'junit:junit:4.12'
+  testImplementation 'com.github.stefanbirkner:system-rules:1.16.0'
 }
 
 configurations.all {
   // ensure SNAPSHOTs are updated every time if needed
   resolutionStrategy.cacheChangingModulesFor 0, 'seconds'
 }
-
+def defaultJvmArgs = ['-Dcache.level1.enabled=false',
+                                '-Dcache.level1.size=0',
+                                '-Dcache.level2.enabled=false',
+                                '-Dcache.level2.size=0',
+                                '--add-exports=java.base/sun.nio.ch=ALL-UNNAMED',
+                                '--add-exports=java.base/jdk.internal.ref=ALL-UNNAMED']
 mainClassName = 'to.wetransform.halecli.CLI'
 applicationName = 'hale'
-applicationDefaultJvmArgs = [
-  '-Dcache.level1.enabled=false',
-  '-Dcache.level1.size=0',
-  '-Dcache.level2.enabled=false',
-  '-Dcache.level2.size=0'
-]
+applicationDefaultJvmArgs = defaultJvmArgs
 
 /*
  * plugin.xml and OSGi manifest
@@ -193,8 +195,8 @@ applicationDefaultJvmArgs = [
  */
 jar {
   manifest {
-    symbolicName = 'to.wetransform.halecli;singleton:=true'
-    instruction 'Bundle-Vendor', 'wetransform GmbH'
+    attributes 'Bundle-SymbolicName': 'to.wetransform.halecli;singleton:=true',
+      'Bundle-Vendor': 'wetransform GmbH'
   }
 }
 
@@ -230,9 +232,14 @@ distributions {
 
 docker {
   javaApplication {
-    baseImage = 'openjdk:8-jre-slim'
+    // https://bmuschko.github.io/gradle-docker-plugin/current/user-guide/#extension_2
+    // switching to jre-jammy as the use pf Alpine as the OS of the hale-cli image breaks derived images that expect Ubuntu
+    baseImage = 'eclipse-temurin:17-jre-jammy'
     maintainer = 'Simon Templer "simon@wetransform.to"'
-    tag = "wetransform/${project.name}:${project.version}"
+    images = ["wetransform/${project.name}:${project.version}", "wetransform/${project.name}:latest"]
+    // apply JAVA_OPTS to docker plugin as the default args configured in build does not apply to docker plugin
+    jvmArgs = defaultJvmArgs
+
   }
 
   url = project.hasProperty('dockerHost') ? dockerHost : 'http://localdocker:2375'
@@ -245,31 +252,14 @@ docker {
   }
 }
 
-dockerPushImage {
-  // workaround for wrong image name used when pushing to docker hub
-  imageName = project.tasks.dockerBuildImage.getTag().split(':')[0]
-  tag = project.tasks.dockerBuildImage.getTag().split(':')[1]
-}
-
-dockerDistTar {
+dockerCreateDockerfile {
   def buildTime = java.time.ZonedDateTime.now().format(java.time.format.DateTimeFormatter.ISO_INSTANT);
   label('git.sha': grgit.head().id, 'git.branch': grgit.branch.current.name, 'build.version': version, 'build.time': buildTime)
+  instruction 'COPY hale /hale/'
 }
 
-// "latest" tag
-
-task dockerTagLatest(type: com.bmuschko.gradle.docker.tasks.image.DockerTagImage,
-    dependsOn: dockerBuildImage) {
-  imageId = "wetransform/${project.name}:${project.version}"
-  repository = "wetransform/${project.name}"
-  tag = 'latest'
-}
-
-task dockerPushLatest(type: com.bmuschko.gradle.docker.tasks.image.DockerPushImage,
-    dependsOn: dockerTagLatest) {
-  imageName = "wetransform/${project.name}"
-  tag = 'latest'
-}
+task dockerTagLatest(dependsOn: dockerBuildImage) {}
+task dockerPushLatest(dependsOn: dockerPushImage) {}
 
 /*
  * Packaging and publishing
@@ -292,58 +282,77 @@ dependencies {
   jansi 'org.fusesource.jansi:jansi:1.11'
 }
 
+task dockerCopyDistResources(type: Copy) {
+  description "Copies the distribution resources to a temporary directory for image creation."
+  dependsOn installDist
+  from installDist.destinationDir.parentFile
+  into dockerCreateDockerfile.destFile.get().asFile.parentFile
+  exclude "**/lib/${jar.archiveFileName}"
+  into("app-lib") {
+    from jar
+  }
+}
+
+tasks.dockerSyncBuildContext {
+  finalizedBy dockerCopyDistResources
+}
+
+tasks.dockerBuildImage {
+  dependsOn dockerCopyDistResources
+}
+
 // package source into a jar file
 task packageSources(type: Jar) {
   from sourceSets.main.allSource
   classifier = 'sources'
 }
 
-// define artifacts for upload
-artifacts {
-  archives jar
-  archives packageJavadoc
-  archives packageSources
-}
-
-// exclude distZip ands distTar artifacts
-configurations.archives.with {
-  artifacts.remove artifacts.find { it.archiveTask.is distZip }
-  artifacts.remove artifacts.find { it.archiveTask.is distTar }
-}
+publishing {
+  publications {
+    mavenJava(MavenPublication) {
+      from components.java
+      artifact packageSources
+      artifact packageJavadoc
+    }
+  }
 
-uploadArchives {
   repositories {
-    mavenDeployer {
-
-      // upload to wetransform artifactory
-      repository(url: 'https://artifactory.wetransform.to/artifactory/libs-release-local') {
-        authentication(userName: project.hasProperty('wetfArtifactoryUser') ? wetfArtifactoryUser : '',
-          password: project.hasProperty('wetfArtifactoryPassword') ? wetfArtifactoryPassword : '')
-      }
-      snapshotRepository(url: 'https://artifactory.wetransform.to/artifactory/libs-snapshot-local') {
-        authentication(userName: project.hasProperty('wetfArtifactoryUser') ? wetfArtifactoryUser : '',
-          password: project.hasProperty('wetfArtifactoryPassword') ? wetfArtifactoryPassword : '')
+    maven {
+      url = project.version.endsWith('-SNAPSHOT') ?
+        'https://artifactory.wetransform.to/artifactory/libs-snapshot-local' :
+        'https://artifactory.wetransform.to/artifactory/libs-release-local'
+      credentials {
+        username project.hasProperty('wetfArtifactoryUser') ? wetfArtifactoryUser : ''
+        password project.hasProperty('wetfArtifactoryPassword') ? wetfArtifactoryPassword : ''
       }
-
     }
   }
 }
 
+// exclude distZip ands distTar artifacts
+configurations.archives.with {
+  artifacts.remove artifacts.find { it.file == 'zip' }
+  artifacts.remove artifacts.find { it.file == 'tar' }
+}
+
 
 // Workaround for gradle application plugin 'the input line is too long' error on Windows
 // see https://gist.github.com/jlmelville/2bfe9277e9e2c0ff79b6
 tasks.withType(CreateStartScripts).each { task ->
   task.doLast {
-      String text = task.windowsScript.text
-      text = text.replaceFirst(/(set CLASSPATH=%APP_HOME%\\lib\\).*/, { "${it[1]}*" })
-      task.windowsScript.write text
+    String text = task.windowsScript.text
+    text = text.replaceFirst(/(set CLASSPATH=%APP_HOME%\\lib\\).*/, { "${it[1]}*" })
+    task.windowsScript.write text
   }
 }
 
+task uploadArchives {
+  dependsOn 'publish'
+}
 
 /*
  * Gradle wrapper
  */
 wrapper {
-  gradleVersion = '3.5'
+  gradleVersion = '7.6.1'
 }
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index d9b7505..943f0cb 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 27fc706..5083229 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
+networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.5-bin.zip
diff --git a/gradlew b/gradlew
index cccdd3d..65dcd68 100755
--- a/gradlew
+++ b/gradlew
@@ -1,78 +1,129 @@
-#!/usr/bin/env sh
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 
 ##############################################################################
-##
-##  Gradle start up script for UN*X
-##
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # Attempt to set APP_HOME
+
 # Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
 
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "`uname`" in
-  CYGWIN* )
-    cygwin=true
-    ;;
-  Darwin* )
-    darwin=true
-    ;;
-  MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
+
 # Determine the Java command to use to start the JVM.
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -81,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
+    JAVACMD=java
     which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
@@ -89,84 +140,105 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
-    if [ $? -eq 0 ] ; then
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
-            MAX_FD="$MAX_FD_LIMIT"
-        fi
-        ulimit -n $MAX_FD
-        if [ $? -ne 0 ] ; then
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
-        fi
-    else
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
-    fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045 
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045 
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
 fi
 
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
     # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
-
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
         fi
-        i=$((i+1))
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
     done
-    case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
-    esac
 fi
 
-# Escape application args
-save () {
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
-    echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
 fi
 
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
 exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
index f955316..93e3f59 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -1,4 +1,20 @@
-@if "%DEBUG%" == "" @echo off
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
 @rem
 @rem  Gradle startup script for Windows
@@ -9,19 +25,23 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if %ERRORLEVEL% equ 0 goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -35,7 +55,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -45,38 +65,26 @@ echo location of your Java installation.
 
 goto fail
 
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
 :execute
 @rem Setup the command line
 
 set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
+
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
diff --git a/src/main/groovy/to/wetransform/halecli/data/RewriteCommand.groovy b/src/main/groovy/to/wetransform/halecli/data/RewriteCommand.groovy
index a3c1a1a..19b6ee2 100644
--- a/src/main/groovy/to/wetransform/halecli/data/RewriteCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/data/RewriteCommand.groovy
@@ -15,50 +15,24 @@
 
 package to.wetransform.halecli.data
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
-import static to.wetransform.halecli.util.HaleIOHelper.*
-
-import java.io.File;
-import java.util.Iterator;
-import java.util.List
-import java.util.concurrent.atomic.AtomicBoolean;
-
-import org.eclipse.core.runtime.NullProgressMonitor;
-import org.eclipse.core.runtime.jobs.IJobChangeEvent
-import org.eclipse.core.runtime.jobs.IJobChangeListener;
-import org.eclipse.core.runtime.jobs.Job;
-import org.eclipse.core.runtime.jobs.JobChangeAdapter;
-
-import com.google.common.io.Files
-
-import eu.esdihumboldt.hale.app.transform.ConsoleProgressMonitor
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
-import eu.esdihumboldt.hale.common.core.io.HaleIO
-import eu.esdihumboldt.hale.common.core.io.Value;
-import eu.esdihumboldt.hale.common.core.io.report.IOReport;
-import eu.esdihumboldt.hale.common.core.io.supplier.FileIOSupplier
-import eu.esdihumboldt.hale.common.headless.transform.AbstractTransformationJob;
-import eu.esdihumboldt.hale.common.instance.graph.reference.ReferenceGraph;
-import eu.esdihumboldt.hale.common.instance.graph.reference.impl.XMLInspector
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
+import eu.esdihumboldt.hale.common.core.io.report.IOReport
 import eu.esdihumboldt.hale.common.instance.io.InstanceWriter
-import eu.esdihumboldt.hale.common.instance.model.DataSet;
-import eu.esdihumboldt.hale.common.instance.model.Filter;
-import eu.esdihumboldt.hale.common.instance.model.Instance;
+import eu.esdihumboldt.hale.common.instance.model.DataSet
 import eu.esdihumboldt.hale.common.instance.model.InstanceCollection
-import eu.esdihumboldt.hale.common.instance.model.impl.FilteredInstanceCollection;
-import eu.esdihumboldt.hale.common.instance.orient.OInstance;
-import eu.esdihumboldt.hale.common.instance.orient.storage.BrowseOrientInstanceCollection;
+import eu.esdihumboldt.hale.common.instance.orient.storage.BrowseOrientInstanceCollection
 import eu.esdihumboldt.hale.common.instance.orient.storage.LocalOrientDB
-import eu.esdihumboldt.hale.common.instance.orient.storage.StoreInstancesJob;
-import eu.esdihumboldt.hale.common.schema.model.Schema;
-import eu.esdihumboldt.hale.common.schema.model.TypeIndex
+import eu.esdihumboldt.hale.common.schema.model.Schema
 import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace
-import eu.esdihumboldt.util.cli.CLIUtil;
+import eu.esdihumboldt.util.cli.CLIUtil
 import eu.esdihumboldt.util.cli.Command
 import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic
+import groovy.cli.picocli.CliBuilder
 import to.wetransform.halecli.util.InstanceCLI
 import to.wetransform.halecli.util.SchemaCLI
+import groovy.cli.picocli.OptionAccessor
+
+import static to.wetransform.halecli.util.HaleIOHelper.guessSchema
 
 /**
  * Reads a source file and writes it.
diff --git a/src/main/groovy/to/wetransform/halecli/data/SplitCommand.groovy b/src/main/groovy/to/wetransform/halecli/data/SplitCommand.groovy
index 0a57375..eca8cae 100644
--- a/src/main/groovy/to/wetransform/halecli/data/SplitCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/data/SplitCommand.groovy
@@ -15,49 +15,30 @@
 
 package to.wetransform.halecli.data
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
-
-import java.io.File;
-import java.util.Iterator;
-import java.util.List
-import java.util.concurrent.atomic.AtomicBoolean;
-
-import org.eclipse.core.runtime.NullProgressMonitor;
-import org.eclipse.core.runtime.jobs.IJobChangeEvent
-import org.eclipse.core.runtime.jobs.IJobChangeListener;
-import org.eclipse.core.runtime.jobs.Job;
-import org.eclipse.core.runtime.jobs.JobChangeAdapter;
-
-import com.google.common.io.Files
-
-import eu.esdihumboldt.hale.app.transform.ConsoleProgressMonitor
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
 import eu.esdihumboldt.hale.common.core.io.HaleIO
-import eu.esdihumboldt.hale.common.core.io.Value;
-import eu.esdihumboldt.hale.common.core.io.report.IOReport;
+import eu.esdihumboldt.hale.common.core.io.Value
+import eu.esdihumboldt.hale.common.core.io.report.IOReport
 import eu.esdihumboldt.hale.common.core.io.supplier.FileIOSupplier
 import eu.esdihumboldt.hale.common.core.report.ReportHandler
-import eu.esdihumboldt.hale.common.headless.transform.AbstractTransformationJob;
-import eu.esdihumboldt.hale.common.instance.graph.reference.ReferenceGraph;
+import eu.esdihumboldt.hale.common.instance.graph.reference.ReferenceGraph
 import eu.esdihumboldt.hale.common.instance.graph.reference.impl.XMLInspector
 import eu.esdihumboldt.hale.common.instance.io.InstanceWriter
-import eu.esdihumboldt.hale.common.instance.model.DataSet;
-import eu.esdihumboldt.hale.common.instance.model.Filter;
-import eu.esdihumboldt.hale.common.instance.model.Instance;
+import eu.esdihumboldt.hale.common.instance.model.DataSet
 import eu.esdihumboldt.hale.common.instance.model.InstanceCollection
-import eu.esdihumboldt.hale.common.instance.model.impl.FilteredInstanceCollection;
-import eu.esdihumboldt.hale.common.instance.orient.OInstance;
-import eu.esdihumboldt.hale.common.instance.orient.storage.BrowseOrientInstanceCollection;
+import eu.esdihumboldt.hale.common.instance.orient.storage.BrowseOrientInstanceCollection
 import eu.esdihumboldt.hale.common.instance.orient.storage.LocalOrientDB
-import eu.esdihumboldt.hale.common.instance.orient.storage.StoreInstancesJob;
-import eu.esdihumboldt.hale.common.schema.model.Schema;
-import eu.esdihumboldt.hale.common.schema.model.TypeIndex
-import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace;
+import eu.esdihumboldt.hale.common.schema.model.Schema
+import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace
 import eu.esdihumboldt.util.cli.Command
 import eu.esdihumboldt.util.cli.CommandContext
+import groovy.cli.picocli.CliBuilder
 import groovy.transform.CompileStatic
 import to.wetransform.halecli.util.InstanceCLI
 import to.wetransform.halecli.util.SchemaCLI
+import groovy.cli.picocli.OptionAccessor
+
+import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
 
 /**
  * Splits a GML source file and creates multiple target files.
diff --git a/src/main/groovy/to/wetransform/halecli/groovy/GroovyShellCommand.groovy b/src/main/groovy/to/wetransform/halecli/groovy/GroovyShellCommand.groovy
index e8e3eb7..0faa513 100644
--- a/src/main/groovy/to/wetransform/halecli/groovy/GroovyShellCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/groovy/GroovyShellCommand.groovy
@@ -16,30 +16,24 @@
 
 package to.wetransform.halecli.groovy
 
-import java.util.List
-
-import org.codehaus.groovy.tools.shell.AnsiDetector;
+import eu.esdihumboldt.cst.functions.groovy.helper.HelperFunctions
+import eu.esdihumboldt.hale.common.core.HalePlatform
+import eu.esdihumboldt.hale.common.core.io.HaleIO
+import eu.esdihumboldt.hale.common.core.io.Value
+import eu.esdihumboldt.util.cli.Command
+import eu.esdihumboldt.util.cli.CommandContext
+import groovy.transform.CompileStatic
+import groovyjarjarcommonscli.HelpFormatter
 import org.codehaus.groovy.tools.shell.Groovysh
 import org.codehaus.groovy.tools.shell.IO
-import org.codehaus.groovy.tools.shell.Main;
-import org.codehaus.groovy.tools.shell.util.HelpFormatter
+import org.codehaus.groovy.tools.shell.Main
 import org.codehaus.groovy.tools.shell.util.Logger
 import org.codehaus.groovy.tools.shell.util.MessageSource
 import org.codehaus.groovy.tools.shell.util.NoExitSecurityManager
 import org.eclipse.core.runtime.IConfigurationElement
-import org.eclipse.core.runtime.Platform;
-import org.fusesource.jansi.Ansi;
-import org.fusesource.jansi.AnsiConsole
-
-import eu.esdihumboldt.cst.functions.groovy.GroovyConstants
-import eu.esdihumboldt.cst.functions.groovy.helper.HelperFunctions
-import eu.esdihumboldt.hale.common.core.HalePlatform;
-import eu.esdihumboldt.hale.common.core.io.HaleIO;
-import eu.esdihumboldt.hale.common.core.io.Value;
-import eu.esdihumboldt.util.cli.Command
-import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic;
-
+import org.eclipse.core.runtime.Platform
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 /**
  * Groovy shell command based on Groovy shell main class.
  *
diff --git a/src/main/groovy/to/wetransform/halecli/project/AbstractDeriveProjectCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/AbstractDeriveProjectCommand.groovy
index 8c6b646..5093cd5 100644
--- a/src/main/groovy/to/wetransform/halecli/project/AbstractDeriveProjectCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/AbstractDeriveProjectCommand.groovy
@@ -15,34 +15,17 @@
 
 package to.wetransform.halecli.project
 
-import org.eclipse.core.runtime.content.IContentType
-
 import eu.esdihumboldt.hale.common.align.model.Alignment
 import eu.esdihumboldt.hale.common.cli.project.AbstractProjectEnvironmentCommand
-import eu.esdihumboldt.hale.common.core.io.HaleIO
-import eu.esdihumboldt.hale.common.core.io.extension.IOProviderDescriptor
-import eu.esdihumboldt.hale.common.core.io.project.ComplexConfigurationService;
-import eu.esdihumboldt.hale.common.core.io.project.ProjectIO;
-import eu.esdihumboldt.hale.common.core.io.project.ProjectWriter
-import eu.esdihumboldt.hale.common.core.io.project.extension.ProjectFileExtension
-import eu.esdihumboldt.hale.common.core.io.project.extension.ProjectFileFactory;
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
-import eu.esdihumboldt.hale.common.core.io.project.model.Project;
-import eu.esdihumboldt.hale.common.core.io.project.model.ProjectFile
-import eu.esdihumboldt.hale.common.core.io.report.IOReport
-import eu.esdihumboldt.hale.common.core.io.supplier.FileIOSupplier;
-import eu.esdihumboldt.hale.common.core.io.supplier.LocatableOutputSupplier
-import eu.esdihumboldt.hale.common.core.report.ReportHandler;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider
-import eu.esdihumboldt.hale.common.headless.HeadlessIO;
-import eu.esdihumboldt.hale.common.headless.impl.HeadlessProjectAdvisor;
+import eu.esdihumboldt.hale.common.core.io.project.ComplexConfigurationService
+import eu.esdihumboldt.hale.common.core.io.project.ProjectIO
+import eu.esdihumboldt.hale.common.core.io.project.model.Project
+import eu.esdihumboldt.hale.common.core.io.supplier.FileIOSupplier
+import eu.esdihumboldt.hale.common.core.report.ReportHandler
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
 import eu.esdihumboldt.util.cli.CommandContext
-import eu.esdihumboldt.util.io.OutputSupplier
-import groovy.transform.CompileStatic;
-import groovy.util.CliBuilder
-import to.wetransform.halecli.project.advisor.SaveProjectAdvisor
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 
 /**
  * Base class for command creating derived projects.
diff --git a/src/main/groovy/to/wetransform/halecli/project/ExportProjectCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/ExportProjectCommand.groovy
index 1a2f517..5942bd0 100644
--- a/src/main/groovy/to/wetransform/halecli/project/ExportProjectCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/ExportProjectCommand.groovy
@@ -15,29 +15,14 @@
 
 package to.wetransform.halecli.project
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions;
-import eu.esdihumboldt.hale.common.align.migrate.impl.DefaultAlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.impl.MigrationOptionsImpl
-import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping;
-import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
-import eu.esdihumboldt.hale.common.core.io.project.model.Project
-import eu.esdihumboldt.hale.common.core.report.SimpleLog;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.instance.io.InstanceIO;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
 import eu.esdihumboldt.util.cli.Command
 import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 import to.wetransform.halecli.util.HaleConnectCLI
-import to.wetransform.halecli.util.ProjectCLI;;;;
+import to.wetransform.halecli.util.ProjectCLI
 
 /**
  * Command exporting a project
diff --git a/src/main/groovy/to/wetransform/halecli/project/alignment/FilterAlignmentCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/alignment/FilterAlignmentCommand.groovy
index 1cff05e..2e4d079 100644
--- a/src/main/groovy/to/wetransform/halecli/project/alignment/FilterAlignmentCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/alignment/FilterAlignmentCommand.groovy
@@ -15,42 +15,32 @@
 
 package to.wetransform.halecli.project.alignment
 
-import javax.xml.namespace.QName
-
 import eu.esdihumboldt.cst.functions.groovy.GroovyJoin
-import eu.esdihumboldt.hale.common.align.migrate.util.MigrationUtil;
-import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.align.model.AlignmentUtil;
-import eu.esdihumboldt.hale.common.align.model.BaseAlignmentCell;
-import eu.esdihumboldt.hale.common.align.model.Cell
-import eu.esdihumboldt.hale.common.align.model.CellUtil;
-import eu.esdihumboldt.hale.common.align.model.Entity
-import eu.esdihumboldt.hale.common.align.model.ModifiableCell;
-import eu.esdihumboldt.hale.common.align.model.MutableAlignment
-import eu.esdihumboldt.hale.common.align.model.MutableCell
-import eu.esdihumboldt.hale.common.align.model.TransformationMode;
+import eu.esdihumboldt.hale.common.align.migrate.util.MigrationUtil
+import eu.esdihumboldt.hale.common.align.model.*
 import eu.esdihumboldt.hale.common.align.model.functions.JoinFunction
 import eu.esdihumboldt.hale.common.align.model.functions.join.JoinParameter
 import eu.esdihumboldt.hale.common.align.model.impl.DefaultAlignment
-import eu.esdihumboldt.hale.common.align.model.impl.DefaultCell;
-import eu.esdihumboldt.hale.common.core.io.ExportProvider;
+import eu.esdihumboldt.hale.common.align.model.impl.DefaultCell
+import eu.esdihumboldt.hale.common.core.io.ExportProvider
 import eu.esdihumboldt.hale.common.core.io.Value
-import eu.esdihumboldt.hale.common.core.io.ValueList;
+import eu.esdihumboldt.hale.common.core.io.ValueList
 import eu.esdihumboldt.hale.common.core.io.project.ComplexConfigurationService
-import eu.esdihumboldt.hale.common.core.io.project.ProjectIO;
+import eu.esdihumboldt.hale.common.core.io.project.ProjectIO
 import eu.esdihumboldt.hale.common.core.io.project.model.Project
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.schema.SchemaSpaceID;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
+import eu.esdihumboldt.hale.common.schema.SchemaSpaceID
+import eu.esdihumboldt.hale.common.schema.io.SchemaIO
 import eu.esdihumboldt.hale.common.schema.model.TypeDefinition
 import eu.esdihumboldt.hale.io.xsd.constraint.XmlElements
-import eu.esdihumboldt.hale.io.xsd.model.XmlElement;
+import eu.esdihumboldt.hale.io.xsd.model.XmlElement
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 import groovy.json.JsonSlurper
-import groovy.transform.CompileStatic;
-import groovy.util.CliBuilder;
-import groovy.util.OptionAccessor;
+import groovy.transform.CompileStatic
 import to.wetransform.halecli.project.AbstractDeriveProjectCommand
-import to.wetransform.halecli.project.AbstractDeriveProjectCommand.DeriveProjectResult
+
+import javax.xml.namespace.QName
 
 /**
  * Command creating a project with a filtered alignment.
diff --git a/src/main/groovy/to/wetransform/halecli/project/match/MatchSchemasCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/match/MatchSchemasCommand.groovy
index 490c143..c1f4f2f 100644
--- a/src/main/groovy/to/wetransform/halecli/project/match/MatchSchemasCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/match/MatchSchemasCommand.groovy
@@ -15,21 +15,17 @@
 
 package to.wetransform.halecli.project.match
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.model.Alignment;
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
+import eu.esdihumboldt.hale.common.align.model.Alignment
 import eu.esdihumboldt.hale.common.core.io.project.model.Project
 import eu.esdihumboldt.hale.common.core.io.supplier.FileIOSupplier
-import eu.esdihumboldt.hale.common.core.report.ReportHandler;
 import eu.esdihumboldt.hale.common.schema.model.Schema
-import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace;
+import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace
 import eu.esdihumboldt.util.cli.Command
 import eu.esdihumboldt.util.cli.CommandContext
-import to.wetransform.halecli.project.ProjectHelper
-import to.wetransform.halecli.project.match.postnas.PostNASSchemaMatcher
-import to.wetransform.halecli.util.ProjectCLI;
-import to.wetransform.halecli.util.SchemaCLI;
+import groovy.cli.picocli.OptionAccessor
+import to.wetransform.halecli.util.ProjectCLI
+import to.wetransform.halecli.util.SchemaCLI
+import groovy.cli.picocli.CliBuilder
 
 abstract class MatchSchemasCommand implements Command {
 
diff --git a/src/main/groovy/to/wetransform/halecli/project/match/postnas/PostNASSchemaMatcher.groovy b/src/main/groovy/to/wetransform/halecli/project/match/postnas/PostNASSchemaMatcher.groovy
index 6429afe..e760215 100644
--- a/src/main/groovy/to/wetransform/halecli/project/match/postnas/PostNASSchemaMatcher.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/match/postnas/PostNASSchemaMatcher.groovy
@@ -15,6 +15,9 @@
 
 package to.wetransform.halecli.project.match.postnas
 
+import com.google.common.collect.ListMultimap
+import eu.esdihumboldt.hale.common.align.model.Entity
+
 import javax.xml.namespace.QName
 
 import com.google.common.collect.ArrayListMultimap
@@ -286,11 +289,11 @@ class PostNASSchemaMatcher implements SchemaMatcher {
 
     def sources = ArrayListMultimap.create()
     sources.put(null, ref)
-    cell.source = sources
+    cell.source = sources as ListMultimap<String, ? extends Entity>
 
     def targets = ArrayListMultimap.create()
     targets.put(null, target)
-    cell.target = targets
+    cell.target = targets as ListMultimap<String, ? extends Entity>
 
     cell.transformationIdentifier = functionId
 
diff --git a/src/main/groovy/to/wetransform/halecli/project/merge/MergeCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/merge/MergeCommand.groovy
index bfc3c5c..5f52d66 100644
--- a/src/main/groovy/to/wetransform/halecli/project/merge/MergeCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/merge/MergeCommand.groovy
@@ -15,31 +15,16 @@
 
 package to.wetransform.halecli.project.merge
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.merge.impl.MatchingMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions;
-import eu.esdihumboldt.hale.common.align.migrate.impl.DefaultAlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.impl.MigrationOptionsImpl
-import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping;
-import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
-import eu.esdihumboldt.hale.common.core.io.project.model.Project;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
+import eu.esdihumboldt.hale.common.align.merge.impl.MatchingMigration
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
+import eu.esdihumboldt.hale.common.core.service.ServiceProvider
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.instance.io.InstanceIO;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
-import eu.esdihumboldt.util.cli.Command
-import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic
-import groovy.transform.TypeCheckingMode;
-import groovy.util.CliBuilder;
-import groovy.util.OptionAccessor
+import eu.esdihumboldt.hale.common.schema.io.SchemaIO
+import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
 import to.wetransform.halecli.project.migrate.AbstractMigratorCommand
-import to.wetransform.halecli.util.ProjectCLI;;;;
+import to.wetransform.halecli.util.ProjectCLI
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 
 /**
  * Command that migrates a project to a different schema.
diff --git a/src/main/groovy/to/wetransform/halecli/project/merge/MergeMigrator.java b/src/main/groovy/to/wetransform/halecli/project/merge/MergeMigrator.java
index f2b4b59..7bfa392 100644
--- a/src/main/groovy/to/wetransform/halecli/project/merge/MergeMigrator.java
+++ b/src/main/groovy/to/wetransform/halecli/project/merge/MergeMigrator.java
@@ -186,13 +186,17 @@ protected Iterable<MutableCell> mergeCell(Cell originalCell, AlignmentMigration
    * @param migrationAlignment if the alignment is the migration alignment
    */
   private void collectAlignmentStatistics(Alignment alignment, boolean migrationAlignment) {
+    if (statistics == null) {
+      return;
+    }
+
     alignment.getCells().forEach(cell -> {
       String function = cell.getTransformationIdentifier();
       FunctionDefinition<?> fun = FunctionUtil.getFunction(function, serviceProvider);
 
       boolean noSource = cell.getSource() == null || cell.getSource().isEmpty();
 
-      statistics.addFunctionUse(fun, migrationAlignment, noSource);
+      statistics.addFunctionUse(function, fun, migrationAlignment, noSource);
     });
   }
 
diff --git a/src/main/groovy/to/wetransform/halecli/project/merge/MergeStatistics.groovy b/src/main/groovy/to/wetransform/halecli/project/merge/MergeStatistics.groovy
index b9c2203..65644b1 100644
--- a/src/main/groovy/to/wetransform/halecli/project/merge/MergeStatistics.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/merge/MergeStatistics.groovy
@@ -152,21 +152,22 @@ class MergeStatistics {
 
   /**
    * Add the use of a specific function (in a cell).
-   * @param fun the function definition
+   * @param functionId the function ID
+   * @param fun the function definition if available
    * @param migrationFunction if the function usage is from the migration alignment
    */
-  public void addFunctionUse(FunctionDefinition fun, boolean migrationFunction, boolean noSource) {
+  public void addFunctionUse(String functionId, FunctionDefinition fun, boolean migrationFunction, boolean noSource) {
     def map = migrationFunction ? migrationFunctions : functions
 
-    String name = fun.displayName
+    String name = fun?.displayName ?: functionId
 
     def entry = map[name]
     if (entry == null) {
       entry = [
         count: 1,
-        id: fun.id,
+        id: functionId,
         noSource: 0,
-        augmenation: fun.augmentation
+        augmentation: fun?.augmentation
       ]
       map[name] = entry
     }
diff --git a/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigrationCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigrationCommand.groovy
index d9dcdbd..bb6d171 100644
--- a/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigrationCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigrationCommand.groovy
@@ -15,28 +15,13 @@
 
 package to.wetransform.halecli.project.migrate
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions;
+import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration
 import eu.esdihumboldt.hale.common.align.migrate.impl.DefaultAlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.impl.MigrationOptionsImpl
-import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping;
-import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
-import eu.esdihumboldt.hale.common.core.io.project.model.Project;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
-import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.instance.io.InstanceIO;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
-import eu.esdihumboldt.util.cli.Command
-import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic
-import groovy.util.OptionAccessor;
-import to.wetransform.halecli.util.ProjectCLI;;;;
-
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
+import eu.esdihumboldt.hale.common.core.service.ServiceProvider
+import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 /**
  * Base class for commands migrating a project to a different schema.
  *
diff --git a/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigratorCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigratorCommand.groovy
index 9c637ec..79aeeee 100644
--- a/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigratorCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/migrate/AbstractMigratorCommand.groovy
@@ -15,28 +15,26 @@
 
 package to.wetransform.halecli.project.migrate
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration;
+import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration
 import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions;
-import eu.esdihumboldt.hale.common.align.migrate.impl.DefaultAlignmentMigrator
+import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions
 import eu.esdihumboldt.hale.common.align.migrate.impl.MigrationOptionsImpl
-import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping;
+import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping
 import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
 import eu.esdihumboldt.hale.common.core.io.project.model.Project
-import eu.esdihumboldt.hale.common.core.report.SimpleLog;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
+import eu.esdihumboldt.hale.common.core.report.SimpleLog
+import eu.esdihumboldt.hale.common.core.service.ServiceProvider
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.instance.io.InstanceIO;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
+import eu.esdihumboldt.hale.common.instance.io.InstanceIO
+import eu.esdihumboldt.hale.common.schema.io.SchemaIO
+import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
 import eu.esdihumboldt.util.cli.Command
 import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic
-import to.wetransform.halecli.util.ProjectCLI;;;;
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
+import to.wetransform.halecli.util.ProjectCLI
 
 /**
  * Base class for commands migrating a project to a different schema.
diff --git a/src/main/groovy/to/wetransform/halecli/project/migrate/MigrateMatchingCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/migrate/MigrateMatchingCommand.groovy
index d8b0ff1..fbe31db 100644
--- a/src/main/groovy/to/wetransform/halecli/project/migrate/MigrateMatchingCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/migrate/MigrateMatchingCommand.groovy
@@ -15,31 +15,14 @@
 
 package to.wetransform.halecli.project.migrate
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.merge.impl.MatchingMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions;
-import eu.esdihumboldt.hale.common.align.migrate.impl.DefaultAlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.impl.MigrationOptionsImpl
-import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping;
-import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
-import eu.esdihumboldt.hale.common.core.io.project.model.Project;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
+import eu.esdihumboldt.hale.common.align.merge.impl.MatchingMigration
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.instance.io.InstanceIO;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
-import eu.esdihumboldt.util.cli.Command
-import eu.esdihumboldt.util.cli.CommandContext
-import groovy.transform.CompileStatic
-import groovy.transform.TypeCheckingMode;
-import groovy.util.CliBuilder;
-import groovy.util.OptionAccessor;
-import to.wetransform.halecli.util.ProjectCLI;;;;
-
+import eu.esdihumboldt.hale.common.schema.io.SchemaIO
+import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
+import groovy.cli.picocli.CliBuilder
+import to.wetransform.halecli.util.ProjectCLI
+import groovy.cli.picocli.OptionAccessor
 /**
  * Command that migrates a project to a different schema.
  *
diff --git a/src/main/groovy/to/wetransform/halecli/project/migrate/ReplaceSourceCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/migrate/ReplaceSourceCommand.groovy
index 9d9dfe5..ea46528 100644
--- a/src/main/groovy/to/wetransform/halecli/project/migrate/ReplaceSourceCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/project/migrate/ReplaceSourceCommand.groovy
@@ -15,33 +15,15 @@
 
 package to.wetransform.halecli.project.migrate
 
-import java.util.List
-
-import eu.esdihumboldt.hale.common.align.merge.impl.DefaultSchemaMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigration;
-import eu.esdihumboldt.hale.common.align.migrate.AlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.MigrationOptions;
-import eu.esdihumboldt.hale.common.align.migrate.impl.DefaultAlignmentMigrator
-import eu.esdihumboldt.hale.common.align.migrate.impl.MigrationOptionsImpl
-import eu.esdihumboldt.hale.common.align.migrate.util.EffectiveMapping;
-import eu.esdihumboldt.hale.common.align.model.Alignment
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
-import eu.esdihumboldt.hale.common.core.io.project.model.Project;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
-import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
-import eu.esdihumboldt.hale.common.instance.io.InstanceIO;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO
-import eu.esdihumboldt.hale.common.schema.model.Schema;
+import eu.esdihumboldt.hale.common.align.merge.impl.DefaultSchemaMigration
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
+import eu.esdihumboldt.hale.common.schema.model.Schema
 import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
-import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace;
-import eu.esdihumboldt.util.cli.Command
-import eu.esdihumboldt.util.cli.CommandContext
+import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace
+import groovy.cli.picocli.CliBuilder
 import groovy.transform.CompileStatic
-import groovy.util.CliBuilder;
-import groovy.util.OptionAccessor;
-import to.wetransform.halecli.util.ProjectCLI
-import to.wetransform.halecli.util.SchemaCLI;;;;;
-
+import to.wetransform.halecli.util.SchemaCLI
+import groovy.cli.picocli.OptionAccessor
 /**
  * Command that migrates a project to a different schema.
  *
@@ -52,7 +34,7 @@ class ReplaceSourceCommand extends AbstractMigrationCommand<DefaultSchemaMigrati
 
   @Override
   protected void addOptions(CliBuilder cli) {
-    // options for loading new source schema
+// options for loading new source schema
     SchemaCLI.loadSchemaOptions(cli, 'schema', 'The new source schema for the project')
   }
 
diff --git a/src/main/groovy/to/wetransform/halecli/schema/RewriteCommand.groovy b/src/main/groovy/to/wetransform/halecli/schema/RewriteCommand.groovy
index 4b8abd2..eae6151 100644
--- a/src/main/groovy/to/wetransform/halecli/schema/RewriteCommand.groovy
+++ b/src/main/groovy/to/wetransform/halecli/schema/RewriteCommand.groovy
@@ -15,14 +15,13 @@
 
 package to.wetransform.halecli.schema
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
-import static to.wetransform.halecli.util.HaleIOHelper.*
-import to.wetransform.halecli.util.SchemaCLI
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
 import eu.esdihumboldt.hale.common.schema.model.Schema
 import eu.esdihumboldt.util.cli.Command
 import eu.esdihumboldt.util.cli.CommandContext
-
+import groovy.cli.picocli.CliBuilder
+import to.wetransform.halecli.util.SchemaCLI
+import groovy.cli.picocli.OptionAccessor
 /**
  * Reads a schema and writes it.
  *
diff --git a/src/main/groovy/to/wetransform/halecli/util/HaleConnectCLI.groovy b/src/main/groovy/to/wetransform/halecli/util/HaleConnectCLI.groovy
index efed521..bf322b2 100644
--- a/src/main/groovy/to/wetransform/halecli/util/HaleConnectCLI.groovy
+++ b/src/main/groovy/to/wetransform/halecli/util/HaleConnectCLI.groovy
@@ -15,13 +15,13 @@
 
 package to.wetransform.halecli.util
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
 import eu.esdihumboldt.hale.common.core.HalePlatform
 import eu.esdihumboldt.hale.common.core.service.ServiceProvider
 import eu.esdihumboldt.hale.io.haleconnect.HaleConnectService
-import eu.esdihumboldt.util.cli.CLIUtil
-import groovy.transform.CompileStatic
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
+
+import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
 
 /**
  * Common utility functions for configuring a hale connect connection.
diff --git a/src/main/groovy/to/wetransform/halecli/util/InstanceCLI.groovy b/src/main/groovy/to/wetransform/halecli/util/InstanceCLI.groovy
index c1623f3..984478d 100644
--- a/src/main/groovy/to/wetransform/halecli/util/InstanceCLI.groovy
+++ b/src/main/groovy/to/wetransform/halecli/util/InstanceCLI.groovy
@@ -15,41 +15,30 @@
 
 package to.wetransform.halecli.util
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail;
-import static to.wetransform.halecli.util.HaleIOHelper.*
-
-import java.io.InputStream
-import java.io.OutputStream;
-import java.net.URI;
-import java.util.Map
-
-import org.eclipse.core.runtime.jobs.Job;
-
 import com.google.common.io.Files
-
 import eu.esdihumboldt.hale.app.transform.ConsoleProgressMonitor
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
-import eu.esdihumboldt.hale.common.core.io.HaleIO
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
 import eu.esdihumboldt.hale.common.core.io.impl.LogProgressIndicator
-import eu.esdihumboldt.hale.common.core.io.report.IOReport;
-import eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier;
-import eu.esdihumboldt.hale.common.core.io.supplier.LocatableInputSupplier
-import eu.esdihumboldt.hale.common.core.io.supplier.LocatableOutputSupplier
-import eu.esdihumboldt.hale.common.core.report.ReportHandler;
-import eu.esdihumboldt.hale.common.core.service.ServiceProvider;
+import eu.esdihumboldt.hale.common.core.io.report.IOReport
+import eu.esdihumboldt.hale.common.core.report.ReportHandler
+import eu.esdihumboldt.hale.common.core.service.ServiceProvider
+import eu.esdihumboldt.hale.common.headless.transform.filter.InstanceFilterDefinition
 import eu.esdihumboldt.hale.common.instance.io.InstanceReader
-import eu.esdihumboldt.hale.common.instance.io.InstanceWriter;
+import eu.esdihumboldt.hale.common.instance.io.InstanceWriter
 import eu.esdihumboldt.hale.common.instance.model.InstanceCollection
 import eu.esdihumboldt.hale.common.instance.orient.storage.LocalOrientDB
-import eu.esdihumboldt.hale.common.instance.orient.storage.StoreInstancesJob;
-import eu.esdihumboldt.hale.common.schema.io.SchemaReader;
-import eu.esdihumboldt.hale.common.schema.model.Schema
+import eu.esdihumboldt.hale.common.instance.orient.storage.StoreInstancesJob
 import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
 import eu.esdihumboldt.hale.common.schema.model.TypeIndex
-import eu.esdihumboldt.util.Pair;
+import eu.esdihumboldt.util.Pair
 import eu.esdihumboldt.util.cli.CLIUtil
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 import groovy.transform.CompileStatic
-import groovy.util.OptionAccessor
+import org.eclipse.core.runtime.jobs.Job
+
+import static to.wetransform.halecli.util.HaleIOHelper.prepareReader
+import static to.wetransform.halecli.util.HaleIOHelper.prepareWriter
 
 /**
  * Common utility functions for setting up a CliBuilder for loading/saving instances.
@@ -58,12 +47,72 @@ import groovy.util.OptionAccessor
  */
 class InstanceCLI {
 
-  static void loadOptions(CliBuilder cli, String argName = 'data', String descr = 'Data to load') {
+  static void loadOptions(CliBuilder cli, String argName = 'data', String descr = 'Data to load', boolean allowFilter = true) {
     cli._(longOpt: argName, args:1, argName:'file-or-URL', descr)
     cli._(longOpt: argName + '-setting', args:2, valueSeparator:'=', argName:'setting=value',
       'Setting for instance reader (optional, repeatable)')
     cli._(longOpt: argName + '-reader', args:1, argName: 'provider-id',
       'Identifier of instance reader to use (otherwise auto-detect)')
+
+    // filter options
+    if (allowFilter) {
+      filterOptions(cli, argName)
+    }
+  }
+
+  static void filterOptions(CliBuilder cli, String argName) {
+    def prefix = argName ? argName + '-' : ''
+    cli._(longOpt: prefix + 'filter', args: 1, argName: 'filter',
+      'Filter expression that is checked against all objects read from the source. The filter language can be specified at the beginning of the filter expression, followed by a colon. If no language is provided explicitly, the expression is assumed to be CQL. If multiple filters are provided an object must only match one of them.')
+    cli._(longOpt: prefix + 'exclude', args: 1, argName: 'filter',
+      'All objects matching the filter will be exlcuded.')
+    cli._(longOpt: prefix + 'filter-on', args: 2, valueSeparator:'=', argName: 'type=filter',
+      'Filter on a specific type only. You can specify the type\'s name with or without namespace. If you want to specify the namespace, wrap it in curly braces and prepend it to the type name.')
+    cli._(longOpt: prefix + 'exclude-type', args: 1, argName: 'type',
+      'Exclude a specific type')
+  }
+
+  static InstanceFilterDefinition createFilter(OptionAccessor options, String argName) {
+    def prefix = argName ? argName + '-' : ''
+    InstanceFilterDefinition res = null
+
+    def filter = options."${prefix}filters" // magic "s" at the end yields a list
+    if (filter) {
+      if (!res) res = new InstanceFilterDefinition();
+
+      filter.each {
+        res.addUnconditionalFilter(it)
+      }
+    }
+
+    filter = options."${prefix}excludes"
+    if (filter) {
+      if (!res) res = new InstanceFilterDefinition();
+
+      filter.each {
+        res.addExcludeFilter(it)
+      }
+    }
+
+    filter = options."${prefix}filter-ons"
+    if (filter) {
+      if (!res) res = new InstanceFilterDefinition();
+
+      filter.toSpreadMap().each { key, value ->
+        res.addTypeFilter(key, value)
+      }
+    }
+
+    filter = options."${prefix}exclude-types"
+    if (filter) {
+      if (!res) res = new InstanceFilterDefinition();
+
+      filter.each {
+        res.addExcludedType(it)
+      }
+    }
+
+    return res
   }
 
   static InstanceCollection load(OptionAccessor options, TypeIndex schema, String argName = 'data') {
@@ -78,7 +127,9 @@ class InstanceCLI {
 
       String customProvider = options."${argName}-reader" ?: null
 
-      return load(loc, settings, customProvider, schema, reports)
+      InstanceFilterDefinition filter = createFilter(options, argName)
+
+      return load(loc, settings, customProvider, schema, reports, filter)
     }
     else {
       return null
@@ -87,7 +138,7 @@ class InstanceCLI {
 
   @CompileStatic
   static InstanceCollection load(URI loc, Map<String, String> settings, String customProvider,
-      TypeIndex schema, ReportHandler reports) {
+      TypeIndex schema, ReportHandler reports, InstanceFilterDefinition filter = null) {
 
     Pair<InstanceReader, String> readerInfo = prepareReader(loc, InstanceReader, settings, customProvider)
     InstanceReader instanceReader = readerInfo.first
@@ -99,7 +150,13 @@ class InstanceCLI {
     IOReport report = instanceReader.execute(null)
     reports?.publishReport(report)
 
-    instanceReader.getInstances()
+    InstanceCollection result = instanceReader.getInstances()
+
+    if (filter) {
+      result = result.select(filter)
+    }
+
+    return result
   }
 
   // save data
diff --git a/src/main/groovy/to/wetransform/halecli/util/ProjectCLI.groovy b/src/main/groovy/to/wetransform/halecli/util/ProjectCLI.groovy
index 1b98c15..978bc94 100644
--- a/src/main/groovy/to/wetransform/halecli/util/ProjectCLI.groovy
+++ b/src/main/groovy/to/wetransform/halecli/util/ProjectCLI.groovy
@@ -15,8 +15,6 @@
 
 package to.wetransform.halecli.util
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
-import to.wetransform.halecli.project.ProjectHelper
 import eu.esdihumboldt.hale.common.align.model.Alignment
 import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
 import eu.esdihumboldt.hale.common.core.io.HaleIO
@@ -25,7 +23,6 @@ import eu.esdihumboldt.hale.common.core.io.project.ProjectWriter
 import eu.esdihumboldt.hale.common.core.io.project.model.Project
 import eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier
 import eu.esdihumboldt.hale.common.core.io.supplier.FileIOSupplier
-import eu.esdihumboldt.hale.common.core.io.supplier.LocatableOutputSupplier;
 import eu.esdihumboldt.hale.common.core.io.supplier.NoStreamOutputSupplier
 import eu.esdihumboldt.hale.common.core.report.ReportHandler
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
@@ -33,7 +30,12 @@ import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
 import eu.esdihumboldt.hale.io.haleconnect.HaleConnectUrnBuilder
 import eu.esdihumboldt.hale.io.haleconnect.project.HaleConnectProjectWriter
 import eu.esdihumboldt.util.cli.CLIUtil
+import groovy.cli.picocli.CliBuilder
+import groovy.cli.picocli.OptionAccessor
 import groovy.transform.CompileStatic
+import to.wetransform.halecli.project.ProjectHelper
+
+import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail
 
 /**
  * Common utility functions for setting up a CliBuilder for loading and saving a project.
diff --git a/src/main/groovy/to/wetransform/halecli/util/SchemaCLI.groovy b/src/main/groovy/to/wetransform/halecli/util/SchemaCLI.groovy
index d52ba6b..3542545 100644
--- a/src/main/groovy/to/wetransform/halecli/util/SchemaCLI.groovy
+++ b/src/main/groovy/to/wetransform/halecli/util/SchemaCLI.groovy
@@ -15,36 +15,24 @@
 
 package to.wetransform.halecli.util
 
-import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail;
-import static to.wetransform.halecli.util.HaleIOHelper.*
-
-import java.io.InputStream
-import java.net.URI;
-import java.util.Map
-
-import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
-import eu.esdihumboldt.hale.common.core.io.HaleIO
-import eu.esdihumboldt.hale.common.core.io.Value
-import eu.esdihumboldt.hale.common.core.io.impl.LogProgressIndicator;
-import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
-import eu.esdihumboldt.hale.common.core.io.report.IOReport;
-import eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier;
-import eu.esdihumboldt.hale.common.core.io.supplier.LocatableInputSupplier;
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil
+import eu.esdihumboldt.hale.common.core.io.impl.LogProgressIndicator
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration
+import eu.esdihumboldt.hale.common.core.io.report.IOReport
 import eu.esdihumboldt.hale.common.core.report.ReportHandler
-import eu.esdihumboldt.hale.common.instance.io.InstanceReader
-import eu.esdihumboldt.hale.common.instance.io.InstanceWriter;
-import eu.esdihumboldt.hale.common.instance.model.InstanceCollection;
-import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
+import eu.esdihumboldt.hale.common.schema.io.SchemaIO
 import eu.esdihumboldt.hale.common.schema.io.SchemaReader
-import eu.esdihumboldt.hale.common.schema.io.SchemaWriter;
+import eu.esdihumboldt.hale.common.schema.io.SchemaWriter
 import eu.esdihumboldt.hale.common.schema.model.Schema
-import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
+import eu.esdihumboldt.hale.common.schema.model.SchemaSpace
 import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace
-import eu.esdihumboldt.util.Pair;
+import eu.esdihumboldt.util.Pair
 import eu.esdihumboldt.util.cli.CLIUtil
+import groovy.cli.picocli.CliBuilder
 import groovy.transform.CompileStatic
-import groovy.util.CliBuilder
-import groovy.util.OptionAccessor;;;;
+import groovy.cli.picocli.OptionAccessor
+import static to.wetransform.halecli.util.HaleIOHelper.prepareReader
+import static to.wetransform.halecli.util.HaleIOHelper.prepareWriter
 
 /**
  * Common utility functions for setting up a CliBuilder for loading a schema.
diff --git a/src/test/groovy/to/wetransform/halecli/data/RewriteCommandTest.groovy b/src/test/groovy/to/wetransform/halecli/data/RewriteCommandTest.groovy
index 00642c4..4494225 100644
--- a/src/test/groovy/to/wetransform/halecli/data/RewriteCommandTest.groovy
+++ b/src/test/groovy/to/wetransform/halecli/data/RewriteCommandTest.groovy
@@ -15,16 +15,16 @@
 
 package to.wetransform.halecli.data
 
-import static org.junit.Assert.*
-
+import eu.esdihumboldt.util.cli.Runner
 import org.junit.BeforeClass
+import org.junit.Ignore
 import org.junit.Rule
 import org.junit.Test
 import org.junit.contrib.java.lang.system.SystemOutRule
-
 import to.wetransform.halecli.internal.Init
-import eu.esdihumboldt.hale.common.core.HalePlatform
-import eu.esdihumboldt.util.cli.Runner
+
+import static org.junit.Assert.assertEquals
+import static org.junit.Assert.assertTrue
 
 /**
  * Tests for rewrite command.
@@ -139,4 +139,271 @@ class RewriteCommandTest {
     }
   }
 
+  @Test
+  void testRewriteFilter() {
+
+    def args = ['data', 'rewrite'];
+
+    args << '--data'
+    args << getClass().getClassLoader().getResource("testdata/inspire2.gml")
+
+    args << '--data-filter'
+    args << "CQL:id = 'A1'"
+
+    def targetFile = File.createTempFile('rewrite', '.gml')
+    args << '--target'
+    args << targetFile.absolutePath
+    args << '--target-writer'
+    args << 'eu.esdihumboldt.hale.io.gml.writer'
+    args << '--target-setting'
+    args << 'xml.pretty=true'
+
+    try {
+      int code = new Runner('hale').run(args as String[])
+
+      // expecting a successful execution
+      assertEquals(0, code)
+
+      assertTrue(targetFile.exists())
+      assertTrue(targetFile.size() > 0)
+
+      def xml = new XmlSlurper().parse(targetFile)
+      def objects = xml.featureMember
+
+      assertEquals(1, objects.size())
+    } finally {
+      targetFile.delete()
+    }
+  }
+
+  @Test
+  void testRewriteFilterList() {
+
+    def args = ['data', 'rewrite'];
+
+    args << '--data'
+    args << getClass().getClassLoader().getResource("testdata/inspire2.gml")
+
+    args << '--data-filter'
+    args << "CQL:id = 'SW1'"
+
+    args << '--data-filter'
+    args << "CQL:id = 'A1'"
+
+    def targetFile = File.createTempFile('rewrite', '.gml')
+    args << '--target'
+    args << targetFile.absolutePath
+    args << '--target-writer'
+    args << 'eu.esdihumboldt.hale.io.gml.writer'
+    args << '--target-setting'
+    args << 'xml.pretty=true'
+
+    try {
+      int code = new Runner('hale').run(args as String[])
+
+      // expecting a successful execution
+      assertEquals(0, code)
+
+      assertTrue(targetFile.exists())
+      assertTrue(targetFile.size() > 0)
+
+      def xml = new XmlSlurper().parse(targetFile)
+      def objects = xml.featureMember
+
+      assertEquals(2, objects.size())
+      def wcs = objects.Watercourse
+      assertEquals(1, wcs.size())
+      def sws = objects.StandingWater
+      assertEquals(1, sws.size())
+    } finally {
+      targetFile.delete()
+    }
+  }
+
+  @Test
+  void testRewriteExcludeType() {
+
+    def args = ['data', 'rewrite'];
+
+    args << '--data'
+    args << getClass().getClassLoader().getResource("testdata/inspire2.gml")
+
+    args << '--data-exclude-type'
+    args << 'Watercourse'
+
+    def targetFile = File.createTempFile('rewrite', '.gml')
+    args << '--target'
+    args << targetFile.absolutePath
+    args << '--target-writer'
+    args << 'eu.esdihumboldt.hale.io.gml.writer'
+    args << '--target-setting'
+    args << 'xml.pretty=true'
+
+    try {
+      int code = new Runner('hale').run(args as String[])
+
+      // expecting a successful execution
+      assertEquals(0, code)
+
+      assertTrue(targetFile.exists())
+      assertTrue(targetFile.size() > 0)
+
+      def xml = new XmlSlurper().parse(targetFile)
+      def objects = xml.featureMember
+
+      assertEquals(1, objects.size())
+      def wcs = objects.Watercourse
+      assertEquals(0, wcs.size())
+      def sws = objects.StandingWater
+      assertEquals(1, sws.size())
+    } finally {
+      targetFile.delete()
+    }
+  }
+
+  @Ignore('Does not succeed due to bug in hale InstanceFilterDefinition - exclude is ignored if no other filter is present')
+  @Test
+  void testRewriteExclude() {
+
+    def args = ['data', 'rewrite'];
+
+    args << '--data'
+    args << getClass().getClassLoader().getResource("testdata/inspire2.gml")
+
+    args << '--data-exclude'
+    args << "\"id\" = 'A2'"
+
+    def targetFile = File.createTempFile('rewrite', '.gml')
+    args << '--target'
+    args << targetFile.absolutePath
+    args << '--target-writer'
+    args << 'eu.esdihumboldt.hale.io.gml.writer'
+    args << '--target-setting'
+    args << 'xml.pretty=true'
+
+    try {
+      int code = new Runner('hale').run(args as String[])
+
+      // expecting a successful execution
+      assertEquals(0, code)
+
+      assertTrue(targetFile.exists())
+      assertTrue(targetFile.size() > 0)
+
+      def xml = new XmlSlurper().parse(targetFile)
+      def objects = xml.featureMember
+
+      assertEquals(3, objects.size())
+      def wcs = objects.Watercourse
+      assertEquals(2, wcs.size())
+      def sws = objects.StandingWater
+      assertEquals(1, sws.size())
+    } finally {
+      targetFile.delete()
+    }
+  }
+
+  @Test
+  void testRewriteExcludeWorkaround() {
+
+    def args = ['data', 'rewrite'];
+
+    args << '--data'
+    args << getClass().getClassLoader().getResource("testdata/inspire2.gml")
+
+    args << '--data-exclude'
+    args << "\"id\" = 'A2'"
+
+    args << '--data-exclude-type'
+    args << 'DoesNotExist'
+
+    def targetFile = File.createTempFile('rewrite', '.gml')
+    args << '--target'
+    args << targetFile.absolutePath
+    args << '--target-writer'
+    args << 'eu.esdihumboldt.hale.io.gml.writer'
+    args << '--target-setting'
+    args << 'xml.pretty=true'
+
+    try {
+      int code = new Runner('hale').run(args as String[])
+
+      // expecting a successful execution
+      assertEquals(0, code)
+
+      assertTrue(targetFile.exists())
+      assertTrue(targetFile.size() > 0)
+
+      def xml = new XmlSlurper().parse(targetFile)
+      def objects = xml.featureMember
+
+      assertEquals(3, objects.size())
+      def wcs = objects.Watercourse
+      assertEquals(2, wcs.size())
+      def sws = objects.StandingWater
+      assertEquals(1, sws.size())
+    } finally {
+      targetFile.delete()
+    }
+  }
+
+  @Test
+  void testRewriteFilterContext() {
+
+    def args = ['data', 'rewrite'];
+
+    args << '--data'
+    args << getClass().getClassLoader().getResource("testdata/inspire2.gml")
+
+    args << '--data-filter'
+    args << '''groovy:
+      def type = instance.definition.name
+      boolean rejected = false
+      if (type) {
+        withContext { c ->
+          def typeMap = c.typeCounts
+          if (!typeMap) {
+            typeMap = [:]
+            c.typeCounts = typeMap
+          }
+          def count = typeMap[type] ?: 0
+          if (count >= 2) { // only keep max 2 per type
+            rejected = true
+          }
+          typeMap[type] = count + 1
+        }
+      }
+      !rejected
+    '''
+
+    def targetFile = File.createTempFile('rewrite', '.gml')
+    args << '--target'
+    args << targetFile.absolutePath
+    args << '--target-writer'
+    args << 'eu.esdihumboldt.hale.io.gml.writer'
+    args << '--target-setting'
+    args << 'xml.pretty=true'
+
+    try {
+      int code = new Runner('hale').run(args as String[])
+
+      // expecting a successful execution
+      assertEquals(0, code)
+
+      assertTrue(targetFile.exists())
+      assertTrue(targetFile.size() > 0)
+
+      def xml = new XmlSlurper().parse(targetFile)
+      def objects = xml.featureMember
+
+      assertEquals(3, objects.size())
+      def wcs = objects.Watercourse
+      assertEquals(2, wcs.size())
+      def sws = objects.StandingWater
+      assertEquals(1, sws.size())
+    } finally {
+      targetFile.delete()
+    }
+  }
+
 }
diff --git a/src/test/resources/testdata/inspire2.gml b/src/test/resources/testdata/inspire2.gml
new file mode 100644
index 0000000..773067e
--- /dev/null
+++ b/src/test/resources/testdata/inspire2.gml
@@ -0,0 +1,187 @@
+<?xml version="1.0" ?>
+<gml:FeatureCollection xmlns:net="http://inspire.ec.europa.eu/schemas/net/4.0" xmlns:hy-n="http://inspire.ec.europa.eu/schemas/hy-n/4.0" xmlns:sc="http://www.interactive-instruments.de/ShapeChange/AppInfo" xmlns:hy="http://inspire.ec.europa.eu/schemas/hy/4.0" xmlns:gco="http://www.isotc211.org/2005/gco" xmlns:om="http://www.opengis.net/om/2.0" xmlns:hfp="http://www.w3.org/2001/XMLSchema-hasFacetAndProperty" xmlns:gml="http://www.opengis.net/gml/3.2" xmlns:ns1="http://www.w3.org/1999/xhtml" xmlns:base="http://inspire.ec.europa.eu/schemas/base/3.3" xmlns:gn="http://inspire.ec.europa.eu/schemas/gn/4.0" xmlns:gmd="http://www.isotc211.org/2005/gmd" xmlns:sr="http://inspire.ec.europa.eu/schemas/sr/4.0" xmlns:hy-p="http://inspire.ec.europa.eu/schemas/hy-p/4.0" xmlns:gsr="http://www.isotc211.org/2005/gsr" xmlns:gts="http://www.isotc211.org/2005/gts" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:gss="http://www.isotc211.org/2005/gss" xmlns:omor="http://inspire.ec.europa.eu/schemas/omor/3.0" xmlns:omop="http://inspire.ec.europa.eu/schemas/omop/3.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" gml:id="_6e6edc1a-158d-4415-8994-c4c003dbe755" xsi:schemaLocation="http://inspire.ec.europa.eu/schemas/hy-p/4.0 http://inspire.ec.europa.eu/schemas/hy-p/4.0/HydroPhysicalWaters.xsd http://www.opengis.net/gml/3.2 http://schemas.opengis.net/gml/3.2.1/deprecatedTypes.xsd">
+  <gml:featureMember>
+    <hy-p:Watercourse gml:id="A1">
+      <gml:description>Contains Ordnance Survey data © Crown copyright and database right 2011</gml:description>
+      <gml:name></gml:name>
+      <hy-p:geographicalName>
+        <gn:GeographicalName>
+          <gn:language>eng</gn:language>
+          <gn:nativeness xlink:href="http://inspire.ec.europa.eu/codelist/NativenessValue/endonym"></gn:nativeness>
+          <gn:nameStatus xlink:href="http://inspire.ec.europa.eu/codelist/NameStatusValue/official"></gn:nameStatus>
+          <gn:sourceOfName nilReason="other:unpopulated" xsi:nil="true"></gn:sourceOfName>
+          <gn:pronunciation nilReason="other:unpopulated" xsi:nil="true"></gn:pronunciation>
+          <gn:spelling>
+            <gn:SpellingOfName>
+              <gn:text></gn:text>
+              <gn:script>Latn</gn:script>
+            </gn:SpellingOfName>
+          </gn:spelling>
+        </gn:GeographicalName>
+      </hy-p:geographicalName>
+      <hy-p:beginLifespanVersion xsi:nil="true"/>
+      <hy-p:geometry>
+        <gml:Polygon gml:id="_f579f3ca-90f9-4da9-b3e2-e4c8af9a4f84" srsName="http://www.opengis.net/def/crs/EPSG/0/25832" srsDimension="2">
+          <gml:exterior>
+            <gml:LinearRing>
+              <gml:posList>-207345.13554061973 6188201.421230434 -207088.75251305848 6188170.108745712 -207079.05134511134 6188169.882136189 -207069.49237461493 6188171.552484499 -207060.44294713344 6188175.05559922 -207052.25082646974 6188180.2568569295 -207045.2308303879 6188186.95637582 -207039.65273247706 6188194.896697085 -207035.7308950388 6188203.772678946 -207033.6160314005 6188213.243223019 -207033.38941418834 6188222.944382441 -207035.0597521289 6188232.503348024 -207038.56285538268 6188241.552774954 -207043.7641022785 6188249.7448995095 -207050.46361265122 6188256.764903343 -207058.4039289998 6188262.343011683 -207067.27991029166 6188266.264860648 -207076.75045823038 6188268.379735156 -207346.58189882734 6188301.335158737 -207355.3819901311 6188301.621076353 -207364.09352927096 6188300.34339694 -207372.44090120192 6188297.5425429335 -207520.13910204603 6188232.858446235 -207724.51641284954 6188199.20473434 -207902.52683724207 6188237.357314383 -207912.1689432416 6188238.451134508 -207921.83917418402 6188237.642855512 -207931.16590836574 6188234.963538198 -207939.79072413384 6188230.516146437 -207947.38217390387 6188224.471590458 -207953.64852161508 6188217.06215895 -207958.34895412554 6188208.572592365 -207961.3028356639 6188199.3291404685 -207962.39664967917 6188189.6870246865 -207961.58836130193 6188180.016787026 -207958.9090327518 6188170.69005021 -207954.46162961132 6188162.06523629 -207948.41706384148 6188154.473792566 -207941.00762561732 6188148.207454177 -207932.5180564077 6188143.507032843 -207923.27460638422 6188140.553162624 -207736.09752724937 6188100.436239479 -207726.90991634503 6188099.35125106 -207717.68087491766 6188099.994804791 -207497.92639998137 6188136.180968051 -207486.11116307578 6188139.681000924 -207345.13554061973 6188201.421230434</gml:posList>
+            </gml:LinearRing>
+          </gml:exterior>
+        </gml:Polygon>
+      </hy-p:geometry>
+      <hy-p:inspireId>
+        <base:Identifier>
+          <base:localId>_d1a6215e-3185-429f-b9b1-f160437e4f99</base:localId>
+          <base:namespace>_example</base:namespace>
+        </base:Identifier>
+      </hy-p:inspireId>
+      <hy-p:origin xsi:nil="true"/>
+      <hy-p:persistence xsi:nil="true"/>
+      <hy-p:tidal xsi:nil="true"/>
+      <hy-p:drainsBasin xsi:nil="true"/>
+      <hy-p:delineationKnown xsi:nil="true"/>
+      <hy-p:length uom="m" xsi:nil="true"></hy-p:length>
+      <hy-p:level xsi:nil="true"/>
+      <hy-p:width>
+        <hy-p:WidthRange>
+          <hy-p:lower uom="m">4.573170731707317</hy-p:lower>
+          <hy-p:upper uom="m">4.573170731707317</hy-p:upper>
+        </hy-p:WidthRange>
+      </hy-p:width>
+    </hy-p:Watercourse>
+  </gml:featureMember>
+  <gml:featureMember>
+    <hy-p:Watercourse gml:id="A2">
+      <gml:description>Contains Ordnance Survey data © Crown copyright and database right 2011</gml:description>
+      <gml:name></gml:name>
+      <hy-p:geographicalName>
+        <gn:GeographicalName>
+          <gn:language>eng</gn:language>
+          <gn:nativeness xlink:href="http://inspire.ec.europa.eu/codelist/NativenessValue/endonym"></gn:nativeness>
+          <gn:nameStatus xlink:href="http://inspire.ec.europa.eu/codelist/NameStatusValue/official"></gn:nameStatus>
+          <gn:sourceOfName nilReason="other:unpopulated" xsi:nil="true"></gn:sourceOfName>
+          <gn:pronunciation nilReason="other:unpopulated" xsi:nil="true"></gn:pronunciation>
+          <gn:spelling>
+            <gn:SpellingOfName>
+              <gn:text></gn:text>
+              <gn:script>Latn</gn:script>
+            </gn:SpellingOfName>
+          </gn:spelling>
+        </gn:GeographicalName>
+      </hy-p:geographicalName>
+      <hy-p:beginLifespanVersion xsi:nil="true"/>
+      <hy-p:geometry>
+        <gml:Polygon gml:id="_f579f3ca-90f9-4da9-b3e2-e4c8af9a4f84" srsName="http://www.opengis.net/def/crs/EPSG/0/25832" srsDimension="2">
+          <gml:exterior>
+            <gml:LinearRing>
+              <gml:posList>-207345.13554061973 6188201.421230434 -207088.75251305848 6188170.108745712 -207079.05134511134 6188169.882136189 -207069.49237461493 6188171.552484499 -207060.44294713344 6188175.05559922 -207052.25082646974 6188180.2568569295 -207045.2308303879 6188186.95637582 -207039.65273247706 6188194.896697085 -207035.7308950388 6188203.772678946 -207033.6160314005 6188213.243223019 -207033.38941418834 6188222.944382441 -207035.0597521289 6188232.503348024 -207038.56285538268 6188241.552774954 -207043.7641022785 6188249.7448995095 -207050.46361265122 6188256.764903343 -207058.4039289998 6188262.343011683 -207067.27991029166 6188266.264860648 -207076.75045823038 6188268.379735156 -207346.58189882734 6188301.335158737 -207355.3819901311 6188301.621076353 -207364.09352927096 6188300.34339694 -207372.44090120192 6188297.5425429335 -207520.13910204603 6188232.858446235 -207724.51641284954 6188199.20473434 -207902.52683724207 6188237.357314383 -207912.1689432416 6188238.451134508 -207921.83917418402 6188237.642855512 -207931.16590836574 6188234.963538198 -207939.79072413384 6188230.516146437 -207947.38217390387 6188224.471590458 -207953.64852161508 6188217.06215895 -207958.34895412554 6188208.572592365 -207961.3028356639 6188199.3291404685 -207962.39664967917 6188189.6870246865 -207961.58836130193 6188180.016787026 -207958.9090327518 6188170.69005021 -207954.46162961132 6188162.06523629 -207948.41706384148 6188154.473792566 -207941.00762561732 6188148.207454177 -207932.5180564077 6188143.507032843 -207923.27460638422 6188140.553162624 -207736.09752724937 6188100.436239479 -207726.90991634503 6188099.35125106 -207717.68087491766 6188099.994804791 -207497.92639998137 6188136.180968051 -207486.11116307578 6188139.681000924 -207345.13554061973 6188201.421230434</gml:posList>
+            </gml:LinearRing>
+          </gml:exterior>
+        </gml:Polygon>
+      </hy-p:geometry>
+      <hy-p:inspireId>
+        <base:Identifier>
+          <base:localId>_d1a6215e-3185-429f-b9b1-f160437e4f99</base:localId>
+          <base:namespace>_example</base:namespace>
+        </base:Identifier>
+      </hy-p:inspireId>
+      <hy-p:origin xsi:nil="true"/>
+      <hy-p:persistence xsi:nil="true"/>
+      <hy-p:tidal xsi:nil="true"/>
+      <hy-p:drainsBasin xsi:nil="true"/>
+      <hy-p:delineationKnown xsi:nil="true"/>
+      <hy-p:length uom="m" xsi:nil="true"></hy-p:length>
+      <hy-p:level xsi:nil="true"/>
+      <hy-p:width>
+        <hy-p:WidthRange>
+          <hy-p:lower uom="m">4.573170731707317</hy-p:lower>
+          <hy-p:upper uom="m">4.573170731707317</hy-p:upper>
+        </hy-p:WidthRange>
+      </hy-p:width>
+    </hy-p:Watercourse>
+  </gml:featureMember>
+  <gml:featureMember>
+    <hy-p:Watercourse gml:id="A3">
+      <gml:description>Contains Ordnance Survey data © Crown copyright and database right 2011</gml:description>
+      <gml:name></gml:name>
+      <hy-p:geographicalName>
+        <gn:GeographicalName>
+          <gn:language>eng</gn:language>
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