updated doc

README.md

@@ -32,36 +32,6 @@ rpt ngs wc file.trig
 ./produce-graphs.sh | ngs head -n 3
 ```
 
-## Canned Queries
-RPT ships with several useful queries on its classpath. Classpath resources can be printed out using `cpcat`. The following snippet shows examples of invocations and their output:
-
-### Overview
-```bash
-$ rpt cpcat spo.rq
-CONSTRUCT WHERE { ?s ?p ?o }
-
-$ rpt cpcat gspo.rq
-CONSTRUCT WHERE { GRAPH ?g { ?s ?p ?o } }
-```
-
-Any resource (query or data) on the classpath can be used as an argument to the `integrate` command:
-
-```
-rpt integrate yourdata.nt spo.rq
-# When spo.rq is executed then the data is queried and printed out on STDOUT
-```
-
-### Reference
-
-The exact definitions can be viewed with `rpt cpcat resource.rq`.
-
-* `spo.rq`: Output triples from the default graph
-* `gspo.rq`: Output quads from the named graphs
-* `tree.rq`: Deterministically replaces all intermediate nodes with blank nodes. Intermediate nodes are those that appear both as subject and as objects. Useful in conjunction with `--out-format turtle/pretty` for formatting e.g. RML.
-* `gtree.rq`: Named graph version of `tree.rq`
-* `rename.rq`: Replaces all occurrences of an IRI in subject and object positions with a different one. Usage (using environment variables): `FROM='urn:from' TO='urn:to' rpt integrate data.nt rename.rq`
-* `count.rq`: Return the sum of the counts of triples in the default graph and quads in the named graphs.
-* `s.rq`: List the distinct subjects in the default graph
 
 ## Example Use Cases
 

docs/getting-started/index.md

@@ -13,7 +13,7 @@ layout: default
 
 You can download RPT as self-contained  Debian or RPM packages from [RPT's GitHub release page](https://github.com/SmartDataAnalytics/RdfProcessingToolkit/releases).
 
-Note, that for running the JAR bundle with the `java` command yourself you need to add the appropriate `--add-opens` declarations. This is documented on the [Building from Source](getting-started/build.html) page.
+Note, that for running the JAR bundle with the `java` command yourself you need to add the appropriate `--add-opens` [JVM Options](build.html#jvm-options) page.
 
 ### Docker
 

docs/index.md

@@ -20,7 +20,7 @@ RPT is Java tool which comes with debian and rpm packaging. It is invoked using
 * [ngs](named-graph-streams): Processor for named graph streams (ngs) which enables processing for collections of named graphs in streaming fashion. Process huge datasets without running into memory issues.
 * [sbs](sparql-binding-streams): Processor for SPARQL binding streams (sbs) which enables processing of SPARQL result sets in streaming fashion. Most prominently for use in aggregating the output of a `ngs map` operation.
 * [rmltk](https://github.com/Scaseco/r2rml-api-jena/tree/jena-5.0.0#usage-of-the-cli-tool): These are the (sub-)commands of our (R2)RML toolkit. The full documentation is available [here](https://github.com/SmartDataAnalytics/r2rml-api-jena).
-* sansa: These are the (sub-)commands of our Semantic Analysis Stack (Stack) - a Big Data RDF Processing Framework. Features parallel execution of RML/SPARQL and TARQL (if the involved sources support it).
+* [sansa]: These are the (sub-)commands of our Semantic Analysis Stack (Stack) - a Big Data RDF Processing Framework. Features parallel execution of RML/SPARQL and TARQL (if the involved sources support it).
 
 
 **Check this [documentation](doc) for the supported SPARQL extensions with many examples**

docs/integrate/canned-queries.md

@@ -0,0 +1,39 @@
+---
+title: Canned Queries
+parent: RDF/SPARQL Processing
+nav_order: 10
+layout: default
+---
+
+## Canned Queries
+RPT ships with several useful queries on its classpath. Classpath resources can be printed out using `cpcat`. The following snippet shows examples of invocations and their output:
+
+### Overview
+```bash
+$ rpt cpcat spo.rq
+CONSTRUCT WHERE { ?s ?p ?o }
+
+$ rpt cpcat gspo.rq
+CONSTRUCT WHERE { GRAPH ?g { ?s ?p ?o } }
+```
+
+Any resource (query or data) on the classpath can be used as an argument to the `integrate` command:
+
+```
+rpt integrate yourdata.nt spo.rq
+# When spo.rq is executed then the data is queried and printed out on STDOUT
+```
+
+### Reference
+
+The exact definitions can be viewed with `rpt cpcat resource.rq`.
+
+* `spo.rq`: Output triples from the default graph.
+* `gspo.rq`: Output quads from the named graphs.
+* `spogspo.rq`: Output all triples followed by all quads.
+* `tree.rq`: Deterministically replaces all intermediate nodes with blank nodes. Intermediate nodes are those that appear both as subject and as objects. Useful in conjunction with `--out-format turtle/pretty` for formatting e.g. RML.
+* `gtree.rq`: Named graph version of `tree.rq`.
+* `rename.rq`: Replaces all occurrences of an IRI in subject and object positions with a different one. Usage (using environment variables): `FROM='urn:from' TO='urn:to' rpt integrate data.nt rename.rq`
+* `count.rq`: Return the sum of the counts of triples in the default graph and quads in the named graphs.
+* `s.rq`: List the distinct subjects in the default graph.
+