diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c17d6f5dd..f3b23ee81 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -8,7 +8,7 @@ env:
   swift_package_resolve: swift package resolve
   swift_build: swift build --build-tests
   swift_test: swift test
-  periphery_scan: ./.build/debug/periphery scan --quiet --skip-build
+  periphery_scan: ./.build/debug/periphery scan --verbose --clean-build
   cache_version: 1
 jobs:
   macOS:
@@ -50,7 +50,9 @@ jobs:
     - name: Test
       run: ${{ env.swift_test }}
     - name: Scan
-      run: ${{ env.periphery_scan }} --strict
+      run: |
+        ls -Rl .
+        ${{ env.periphery_scan }} --strict
   linux:
     strategy:
       fail-fast: false
diff --git a/Sources/Indexer/SourceFileCollector.swift b/Sources/Indexer/SourceFileCollector.swift
index d02a82095..7bfdf9a59 100644
--- a/Sources/Indexer/SourceFileCollector.swift
+++ b/Sources/Indexer/SourceFileCollector.swift
@@ -33,19 +33,23 @@ public struct SourceFileCollector {
                 let units = indexStore.units(includeSystem: false)
 
                 return try units.compactMap { unit -> (FilePath, IndexStore, IndexStoreUnit, String?)? in
-                    guard let filePath = try indexStore.mainFilePath(for: unit), !filePath.isEmpty else { return nil }
+                    guard let filePath = try indexStore.mainFilePath(for: unit), !filePath.isEmpty else {
+                        return nil
+                    }
 
                     let file = FilePath.makeAbsolute(filePath, relativeTo: currentFilePath)
 
-                    if file.exists {
-                        if !isExcluded(file) {
-                            let module = try indexStore.moduleName(for: unit)
-                            if let module, excludedTargets.contains(module) {
-                                return nil
-                            }
+                    guard file.exists else {
+                        throw PeripheryError.pathDoesNotExist(path: file.string)
+                    }
 
-                            return (file, indexStore, unit, module)
+                    if !isExcluded(file) {
+                        let module = try indexStore.moduleName(for: unit)
+                        if let module, excludedTargets.contains(module) {
+                            return nil
                         }
+
+                        return (file, indexStore, unit, module)
                     }
 
                     return nil
diff --git a/bazel/internal/scan.bzl b/bazel/internal/scan.bzl
index 438f43e9b..3dad901d7 100644
--- a/bazel/internal/scan.bzl
+++ b/bazel/internal/scan.bzl
@@ -5,6 +5,7 @@ load("@rules_apple//apple:providers.bzl", "AppleResourceInfo")
 PeripheryInfo = provider(
     doc = "Provides inputs needed to generate a generic project configuration file.",
     fields = {
+        "swift_srcs": "A depset of Swift source files.",
         "indexstores": "A depset of .indexstore files.",
         "plists": "A depset of .plist files.",
         "xibs": "A depset of .xib and .storyboard files.",
@@ -32,6 +33,7 @@ _force_indexstore = transition(
 )
 
 def _scan_inputs_aspect_impl(target, ctx):
+    swift_srcs = []
     indexstores = []
     test_targets = []
     plists = []
@@ -43,6 +45,9 @@ def _scan_inputs_aspect_impl(target, ctx):
         if SwiftInfo in target and hasattr(target[SwiftInfo], "direct_modules"):
             for module in target[SwiftInfo].direct_modules:
                 if hasattr(module, "swift"):
+                    if hasattr(module.compilation_context, "direct_sources"):
+                        swift_srcs.extend([src for src in module.compilation_context.direct_sources if src.extension == "swift"])
+
                     if ctx.rule.attr.testonly:
                         test_targets.append(module.name)
 
@@ -76,6 +81,10 @@ def _scan_inputs_aspect_impl(target, ctx):
 
     deps = getattr(ctx.rule.attr, "deps", [])
 
+    swift_srcs_depset = depset(
+        swift_srcs,
+        transitive = [dep[PeripheryInfo].swift_srcs for dep in deps],
+    )
     indexstores_depset = depset(
         indexstores,
         transitive = [dep[PeripheryInfo].indexstores for dep in deps],
@@ -103,6 +112,7 @@ def _scan_inputs_aspect_impl(target, ctx):
 
     return [
         PeripheryInfo(
+            swift_srcs = swift_srcs_depset,
             indexstores = indexstores_depset,
             plists = plists_depset,
             xibs = xibs_depset,
@@ -113,6 +123,7 @@ def _scan_inputs_aspect_impl(target, ctx):
     ]
 
 def _scan_impl(ctx):
+    swift_srcs_set = sets.make()
     indexstores_set = sets.make()
     plists_set = sets.make()
     xibs_set = sets.make()
@@ -121,6 +132,7 @@ def _scan_impl(ctx):
     test_targets_set = sets.make()
 
     for dep in ctx.attr.deps:
+        swift_srcs_set = sets.union(swift_srcs_set, sets.make(dep[PeripheryInfo].swift_srcs.to_list()))
         indexstores_set = sets.union(indexstores_set, sets.make(dep[PeripheryInfo].indexstores.to_list()))
         plists_set = sets.union(plists_set, sets.make(dep[PeripheryInfo].plists.to_list()))
         xibs_set = sets.union(xibs_set, sets.make(dep[PeripheryInfo].xibs.to_list()))
@@ -128,6 +140,7 @@ def _scan_impl(ctx):
         xcmappingmodels_set = sets.union(xcmappingmodels_set, sets.make(dep[PeripheryInfo].xcmappingmodels.to_list()))
         test_targets_set = sets.union(test_targets_set, sets.make(dep[PeripheryInfo].test_targets.to_list()))
 
+    swift_srcs = sets.to_list(swift_srcs_set)
     indexstores = sets.to_list(indexstores_set)
     plists = sets.to_list(plists_set)
     xibs = sets.to_list(xibs_set)
@@ -164,13 +177,16 @@ def _scan_impl(ctx):
             [ctx.outputs.scan, project_config_file],
         ),
         runfiles = ctx.runfiles(
-            files = indexstores + plists + xibs + xcdatamodels + xcmappingmodels,
+            # Swift sources are not included in the generate project file, yet they are referenced
+            # in the indexstores and will be read by Periphery, and therefore must be present in
+            # the runfiles.
+            files = swift_srcs + indexstores + plists + xibs + xcdatamodels + xcmappingmodels,
         )
     )
 
 scan_inputs_aspect = aspect(
     _scan_inputs_aspect_impl,
-    attr_aspects = ["deps"],
+    attr_aspects = ["deps", "swift_target"],
 )
 
 scan = rule(