From b9743c8e5b8f53f4f7318fe9ea47b241cb75336d Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Mon, 12 Aug 2024 10:15:21 +0200
Subject: [PATCH 01/16] Auto detect neo4j directory to start/stop a not yet
 updated version

---
 scripts/startNeo4j.sh | 27 +++++++++++++++++++--------
 scripts/stopNeo4j.sh  | 28 ++++++++++++++++++++--------
 2 files changed, 39 insertions(+), 16 deletions(-)

diff --git a/scripts/startNeo4j.sh b/scripts/startNeo4j.sh
index 17be4be1c..890ac5d70 100755
--- a/scripts/startNeo4j.sh
+++ b/scripts/startNeo4j.sh
@@ -10,17 +10,12 @@
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -o errexit -o pipefail
 
+# Overrideable Defaults
 NEO4J_EDITION=${NEO4J_EDITION:-"community"} # Choose "community" or "enterprise"
 NEO4J_VERSION=${NEO4J_VERSION:-"5.21.2"}
 TOOLS_DIRECTORY=${TOOLS_DIRECTORY:-"tools"} # Get the tools directory (defaults to "tools")
 NEO4J_HTTP_PORT=${NEO4J_HTTP_PORT:-"7474"} # Neo4j's own "Bolt Protocol" port
 
-# Internal Constants
-NEO4J_DIR="${TOOLS_DIRECTORY}/neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
-NEO4J_DIR_WINDOWS="${TOOLS_DIRECTORY}\neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
-NEO4J_BIN="${NEO4J_DIR}/bin"
-NEO4J_BIN_WINDOWS="${NEO4J_DIR_WINDOWS}\bin"
-
 ## Get this "scripts" directory if not already set
 # Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
 # CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
@@ -34,6 +29,22 @@ if [ -z "${TOOLS_DIRECTORY}" ]; then
     exit 1
 fi
 
+# Detect Neo4j directory within the "tools" directory
+neo4j_directory="neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}" # Default directory using environment variables
+if [ ! -d "${TOOLS_DIRECTORY}/${neo4j_directory}" ] ; then
+    # Default directory doesn't exist. Try to find one with another version.
+    # This usually happens when Neo4j had been updated while a local project is still using an older version.
+    neo4j_directories=$(find "./${TOOLS_DIRECTORY}" -type d -name "neo4j-${NEO4J_EDITION}-*" | sort -r | head -n 1) 
+    neo4j_directory=$(basename -- "$neo4j_directories")
+    echo "startNeo4j: Auto detected Neo4j directory within the tools directory: ${neo4j_directory}"
+fi
+
+# Internal Constants
+NEO4J_DIR="${TOOLS_DIRECTORY}/${neo4j_directory}"
+NEO4J_DIR_WINDOWS="${TOOLS_DIRECTORY}\\${neo4j_directory}"
+NEO4J_BIN="${NEO4J_DIR}/bin"
+NEO4J_BIN_WINDOWS="${NEO4J_DIR_WINDOWS}\bin"
+
 # Check if Neo4j is installed
 if [ -d "${NEO4J_BIN}" ] ; then
     echo "startNeo4j: Using Neo4j binary directory ${NEO4J_BIN}"
@@ -51,7 +62,7 @@ source "${SCRIPTS_DIR}/waitForNeo4jHttpFunctions.sh"
 # Check if Neo4j is stopped (not running) using a temporary NEO4J_HOME environment variable that points to the current installation
 isDatabaseReady=$(isDatabaseQueryable)
 if [[ ${isDatabaseReady} == "false" ]]; then
-    echo "startNeo4j: Starting neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} in ${NEO4J_DIR}"
+    echo "startNeo4j: Starting ${neo4j_directory} in ${NEO4J_DIR}"
 
     # Check if there is already a process that listens to the Neo4j HTTP port
     if isWindows; then
@@ -88,5 +99,5 @@ if [[ ${isDatabaseReady} == "false" ]]; then
    waitUntilDatabaseIsQueryable
    
 else
-    echo "startNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} already started"
+    echo "startNeo4j: ${neo4j_directory} already started"
 fi
\ No newline at end of file
diff --git a/scripts/stopNeo4j.sh b/scripts/stopNeo4j.sh
index 2746fe0eb..bf7eda7d6 100755
--- a/scripts/stopNeo4j.sh
+++ b/scripts/stopNeo4j.sh
@@ -9,6 +9,7 @@
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -o errexit -o pipefail
 
+# Overrideable Defaults
 NEO4J_EDITION=${NEO4J_EDITION:-"community"} # Choose "community" or "enterprise"
 NEO4J_VERSION=${NEO4J_VERSION:-"5.21.2"}
 TOOLS_DIRECTORY=${TOOLS_DIRECTORY:-"tools"} # Get the tools directory (defaults to "tools")
@@ -21,16 +22,27 @@ NEO4J_HTTP_PORT=${NEO4J_HTTP_PORT:-"7474"}
 SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
 echo "stopNeo4j: SCRIPTS_DIR=$SCRIPTS_DIR"
 
-# Internal Constants
-NEO4J_DIR="${TOOLS_DIRECTORY}/neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
-NEO4J_BIN="${NEO4J_DIR}/bin"
-
 # Check if TOOLS_DIRECTORY variable is set
 if [ -z "${TOOLS_DIRECTORY}" ]; then
     echo "stopNeo4j: Requires variable TOOLS_DIRECTORY to be set. If it is the current directory, then use a dot to reflect that."
     exit 1
 fi
 
+# Detect Neo4j directory within the "tools" directory
+# If the version had been updated and a local project still uses the 
+neo4j_directory="neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}" # Default directory using environment variables
+if [ ! -d "${TOOLS_DIRECTORY}/${neo4j_directory}" ] ; then
+    # Default directory doesn't exist. Try to find one with another version.
+    # This usually happens when Neo4j had been updated while a local project is still using an older version.
+    neo4j_directories=$(find "./${TOOLS_DIRECTORY}" -type d -name "neo4j-${NEO4J_EDITION}-*" | sort -r | head -n 1) 
+    neo4j_directory=$(basename -- "$neo4j_directories")
+    echo "stopNeo4j: Auto detected Neo4j directory within the tools directory: ${neo4j_directory}"
+fi
+
+# Internal Constants
+NEO4J_DIR="${TOOLS_DIRECTORY}/${neo4j_directory}"
+NEO4J_BIN="${NEO4J_DIR}/bin"
+
 # Check if Neo4j is installed
 if [ -d "${NEO4J_BIN}" ] ; then
     echo "stopNeo4j: Using Neo4j binary directory ${NEO4J_BIN}"
@@ -48,11 +60,11 @@ source "${SCRIPTS_DIR}/waitForNeo4jHttpFunctions.sh"
 # Check if Neo4j is stopped (not running) using a temporary NEO4J_HOME environment variable that points to the current installation
 isDatabaseReady=$(isDatabaseQueryable)
 if [[ ${isDatabaseReady} == "false" ]]; then
-    echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} already stopped"
+    echo "stopNeo4j: ${neo4j_directory} already stopped"
     exit 0
 else
     if isWindows; then
-        echo "stopNeo4j: IMPORTANT on Windows: Please close the console window or stop the service manually where neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} is running."
+        echo "stopNeo4j: IMPORTANT on Windows: Please close the console window or stop the service manually where ${neo4j_directory} is running."
     else
         # Stop Neo4j using a temporary NEO4J_HOME environment variable that points to the current installation
         NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j stop
@@ -62,10 +74,10 @@ fi
 # Check if Neo4j is still not running using a temporary NEO4J_HOME environment variable that points to the current installation
 isDatabaseReady=$(isDatabaseQueryable)
 if [[ ${isDatabaseReady} == "false" ]]; then
-    echo "stopNeo4j: Successfully stopped neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
+    echo "stopNeo4j: Successfully stopped ${neo4j_directory}"
 else
     if ! isWindows; then
-        echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} still running. Something went wrong. Details see 'NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j${scriptExtension} status'."
+        echo "stopNeo4j: ${neo4j_directory} still running. Something went wrong. Details see 'NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j${scriptExtension} status'."
         exit 1
     fi
 fi

From 2b1eae0e2fd285ee6cbf46e3886a2d9478efc3e9 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Tue, 13 Aug 2024 08:24:16 +0200
Subject: [PATCH 02/16] Ignore .DS_Store files while scanning

---
 scripts/configuration/template-neo4jv4-jqassistant.yaml | 1 +
 scripts/configuration/template-neo4jv5-jqassistant.yaml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/scripts/configuration/template-neo4jv4-jqassistant.yaml b/scripts/configuration/template-neo4jv4-jqassistant.yaml
index 018b004da..c31732b5d 100644
--- a/scripts/configuration/template-neo4jv4-jqassistant.yaml
+++ b/scripts/configuration/template-neo4jv4-jqassistant.yaml
@@ -131,6 +131,7 @@ jqassistant:
     # -Djqassistant.scan.properties
     properties:
       # plugin.property.key: value
+      file.exclude: "*/.DS_Store"
       json.file.exclude: "*/.reports/jqa/ts-output.json"
 
   # The analyze configuration
diff --git a/scripts/configuration/template-neo4jv5-jqassistant.yaml b/scripts/configuration/template-neo4jv5-jqassistant.yaml
index 67474a47a..d73be1db5 100644
--- a/scripts/configuration/template-neo4jv5-jqassistant.yaml
+++ b/scripts/configuration/template-neo4jv5-jqassistant.yaml
@@ -131,6 +131,7 @@ jqassistant:
     # -Djqassistant.scan.properties
     properties:
       # plugin.property.key: value
+      file.exclude: "*/.DS_Store"
       json.file.exclude: "*/.reports/jqa/ts-output.json"
 
   # The analyze configuration

From 4cb0cacf631ea2e045786c7a680e0073392ab3c9 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Tue, 13 Aug 2024 20:11:13 +0200
Subject: [PATCH 03/16] Delete plain files in .git directory since they can't
 be ignored for now.

Related to: https://github.com/jQAssistant/jqassistant/issues/410
---
 .../Delete_plain_git_directory_file_nodes.cypher   | 14 ++++++++++++++
 scripts/importGit.sh                               | 12 ++++++++++++
 2 files changed, 26 insertions(+)
 create mode 100644 cypher/GitLog/Delete_plain_git_directory_file_nodes.cypher

diff --git a/cypher/GitLog/Delete_plain_git_directory_file_nodes.cypher b/cypher/GitLog/Delete_plain_git_directory_file_nodes.cypher
new file mode 100644
index 000000000..f8baf7da0
--- /dev/null
+++ b/cypher/GitLog/Delete_plain_git_directory_file_nodes.cypher
@@ -0,0 +1,14 @@
+// Delete plain file nodes in "/.git" directory
+
+MATCH (git_metadata_file:File)<-[:CONTAINS*]-(git_directory:Directory)
+WHERE git_directory.fileName ENDS WITH '/.git'
+ WITH git_directory.fileName AS gitDirectory
+     ,count(DISTINCT git_metadata_file.fileName)          AS numberOfFiles
+     ,collect(DISTINCT git_metadata_file.fileName)[0..4]  AS fileExamples
+     ,collect(DISTINCT git_metadata_file)                 AS git_metadata_files
+UNWIND git_metadata_files AS git_metadata_file
+  CALL { WITH git_metadata_file
+         DETACH DELETE git_metadata_file
+       } IN TRANSACTIONS OF 1000 ROWS
+RETURN DISTINCT gitDirectory, numberOfFiles, fileExamples
+ORDER BY numberOfFiles DESC
\ No newline at end of file
diff --git a/scripts/importGit.sh b/scripts/importGit.sh
index c144cc976..884d30e77 100755
--- a/scripts/importGit.sh
+++ b/scripts/importGit.sh
@@ -135,12 +135,24 @@ postGitLogImport() {
 
 postGitPluginImport() {
   echo "importGit: Creating indexes for plugin-provided git data..."
+
+  # TODO: The deletion of all plain files in the "/.git" directory is needed
+  #       until there is a way to exclude all files inside a directory
+  #       while still being able to get them analyzed by the git plugin.
+  #       This would most likely be solved with https://github.com/jQAssistant/jqassistant/issues/410
+  execute_cypher "${GIT_LOG_CYPHER_DIR}/Delete_plain_git_directory_file_nodes.cypher"
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_commit_sha.cypher"
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_file_name.cypher"
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_file_relative_path.cypher"
 
   commonPostGitImport
 
+  #TODO Add verification steps
+  #verificationResult=$( execute_cypher_http_number_of_lines_in_result "${GIT_LOG_CYPHER_DIR}/Verify_code_to_git_file_unambiguous.cypher" )
+  #if [ "${verificationResult}" != 0 ]; then
+  #  echo "importGit: Error: Verification failed. Git:File->!Git:File RESOLVES_TO relationships ambiguous"
+  #fi
+
   echo "importGit: Add numberOfGitCommits property to nodes with matching file names..."
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Set_number_of_git_plugin_commits.cypher"
 }

From 9f22f7b45e42371fc4e508de7e387edfa5766744 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 17:24:43 +0200
Subject: [PATCH 04/16] Fix git file matching ambiguity for multi repository
 analysis

---
 ...relationships_to_git_files_for_Java.cypher | 25 ++++++++++++-----
 ...onships_to_git_files_for_Typescript.cypher | 27 ++++++++++++++-----
 .../Import_aggregated_git_log_csv_data.cypher |  2 +-
 cypher/GitLog/Import_git_log_csv_data.cypher  |  2 +-
 ...les_by_resolved_label_and_extension.cypher | 14 ++++++++++
 ...Verify_code_to_git_file_unambiguous.cypher | 16 +++++++++++
 ...Verify_git_to_code_file_unambiguous.cypher | 17 ++++++++++++
 scripts/importGit.sh                          | 12 ++++-----
 8 files changed, 93 insertions(+), 22 deletions(-)
 create mode 100644 cypher/GitLog/List_git_files_by_resolved_label_and_extension.cypher
 create mode 100644 cypher/GitLog/Verify_code_to_git_file_unambiguous.cypher
 create mode 100644 cypher/GitLog/Verify_git_to_code_file_unambiguous.cypher

diff --git a/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Java.cypher b/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Java.cypher
index 353888f6f..5085f852a 100644
--- a/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Java.cypher
+++ b/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Java.cypher
@@ -1,12 +1,18 @@
-// Connect git files to code files with a RESOLVES_TO relationship if their names match
-// Note: Even if is tempting to combine this file with the Typescript variant, they are intentionally spearated.
+// Connect git files to Java code files with a RESOLVES_TO relationship if their names match
+// Note: Its quite tricky to match Java class file paths from inside e.g. *.jar files to their source repository file path reliable.
+//       This could be improved by utilizing package manager data (like maven). Even that turns out to be not easy,
+//       since the folder structure can be customized. Therefore, this is only a simplified attempt and by no means complete.
+// Note: Even if is tempting to combine this file with the Typescript variant, they are intentionally separated.
 //       The differences are subtle but need to be thought through and tested carefully.
 //       Having separate files makes it obvious that there needs to be one for every new source code language.
 
-MATCH (code_file:File&!Git)
-WHERE NOT EXISTS { (code_file)-[:RESOLVES_TO]->(other_file:File&!Git) } // only original nodes, no duplicates
- WITH code_file, replace(code_file.fileName, '.class', '.java') AS codeFileName
-MATCH (git_file:File&Git)
+MATCH (code_file:!Git&File)
+WHERE  code_file.fileName IS NOT NULL
+  // Use only original code files, no resolved duplicates
+  AND NOT EXISTS { (code_file)-[:RESOLVES_TO]->(other_file:File&!Git) }
+ WITH code_file
+     ,replace(code_file.fileName, '.class', '.java') AS codeFileName
+MATCH (git_file:Git&File)
  WITH *
      ,git_file
      ,coalesce(git_file.fileName, git_file.relativePath) AS gitFileName
@@ -14,4 +20,9 @@ WHERE gitFileName ENDS WITH codeFileName
 MERGE (git_file)-[:RESOLVES_TO]->(code_file)
   SET git_file.resolved = true
 RETURN count(DISTINCT codeFileName)  AS numberOfCodeFiles
-      ,collect(DISTINCT codeFileName + ' <-> ' + gitFileName + '\n')[0..4] AS examples
\ No newline at end of file
+      ,collect(DISTINCT codeFileName + ' <-> ' + gitFileName + '\n')[0..4] AS examples
+// RETURN codeFileName, gitFileName
+//       ,git_file.fileName, git_file.relativePath
+//       ,git_repository.fileName , code_file.absoluteFileName
+//       ,git_repository.name, code_file.fileName
+// LIMIT 20
\ No newline at end of file
diff --git a/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Typescript.cypher b/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Typescript.cypher
index d7f8d4495..11f249d55 100644
--- a/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Typescript.cypher
+++ b/cypher/GitLog/Add_RESOLVES_TO_relationships_to_git_files_for_Typescript.cypher
@@ -1,17 +1,30 @@
 // Connect git files to Typescript files with a RESOLVES_TO relationship if their names match
-// Note: Even if is tempting to combine this file with the Java variant, they are intentionally spearated.
+// Note: Even if is tempting to combine this file with the Java variant, they are intentionally separated.
 //       The differences are subtle but need to be thought through and tested carefully.
 //       Having separate files makes it obvious that there needs to be one for every new source code language.
 
-MATCH (code_file:File&!Git)
-WHERE NOT EXISTS { (code_file)-[:RESOLVES_TO]->(other_file:File&!Git) } // only original nodes, no duplicates
- WITH code_file, code_file.absoluteFileName AS codeFileName
-MATCH (git_file:File&Git)
+MATCH (code_file:!Git&File)
+WHERE (code_file.absoluteFileName IS NOT NULL OR code_file.fileName IS NOT NULL)
+  // Use only original code files, no resolved duplicates
+  AND NOT EXISTS { (code_file)-[:RESOLVES_TO]->(other_file:File&!Git) } 
+ WITH code_file
+     ,coalesce(code_file.absoluteFileName, code_file.fileName) AS codeFileName
+MATCH (git_file:Git&File)
+// Use repository if available to overcome ambiguity in multi source analysis
+OPTIONAL MATCH (git_repository:Git&Repository)-[:HAS_FILE]->(git_file)
  WITH *
+     ,git_repository
      ,git_file
-     ,coalesce(git_file.fileName, git_file.relativePath) AS gitFileName
+     ,coalesce(coalesce(git_repository.fileName + '/', '')  + git_file.fileName
+              ,coalesce(git_repository.name + '/', '')      + git_file.relativePath
+      ) AS gitFileName
 WHERE codeFileName      ENDS WITH gitFileName
 MERGE (git_file)-[:RESOLVES_TO]->(code_file)
   SET git_file.resolved = true
 RETURN count(DISTINCT codeFileName)  AS numberOfCodeFiles
-      ,collect(DISTINCT codeFileName + ' <-> ' + gitFileName + '\n')[0..4] AS examples
\ No newline at end of file
+      ,collect(DISTINCT codeFileName + ' <-> ' + gitFileName + '\n')[0..4] AS examples
+// RETURN codeFileName, gitFileName
+//       ,git_file.fileName, git_file.relativePath
+//       ,git_repository.fileName , code_file.absoluteFileName
+//       ,git_repository.name, code_file.fileName
+// LIMIT 20
\ No newline at end of file
diff --git a/cypher/GitLog/Import_aggregated_git_log_csv_data.cypher b/cypher/GitLog/Import_aggregated_git_log_csv_data.cypher
index b9f0de283..2db4a4956 100644
--- a/cypher/GitLog/Import_aggregated_git_log_csv_data.cypher
+++ b/cypher/GitLog/Import_aggregated_git_log_csv_data.cypher
@@ -9,7 +9,7 @@ CALL { WITH row
         month:   toInteger(row.month),
         commits: toInteger(row.commits)
     })
-    MERGE (git_file:Git:Log:File {fileName: row.filename})
+    MERGE (git_file:Git:Log:File {fileName: row.filename, repositoryPath: $git_repository_absolute_directory_name})
     MERGE (git_author)-[:AUTHORED]->(git_change_span)
     MERGE (git_change_span)-[:CONTAINS_CHANGED]->(git_file)
     MERGE (git_repository)-[:HAS_CHANGE_SPAN]->(git_change_span)
diff --git a/cypher/GitLog/Import_git_log_csv_data.cypher b/cypher/GitLog/Import_git_log_csv_data.cypher
index 77e6ca3a3..3bd448671 100644
--- a/cypher/GitLog/Import_git_log_csv_data.cypher
+++ b/cypher/GitLog/Import_git_log_csv_data.cypher
@@ -12,7 +12,7 @@ CALL { WITH row
         timestamp:      datetime(row.timestamp),
         timestamp_unix: toInteger(row.timestamp_unix)
     })
-    MERGE (git_file:Git:Log:File {fileName: row.filename})
+    MERGE (git_file:Git:Log:File {fileName: row.filename, repositoryPath: $git_repository_absolute_directory_name})
     MERGE (git_author)-[:AUTHORED]->(git_commit)
     MERGE (git_commit)-[:CONTAINS_CHANGED]->(git_file)
     MERGE (git_repository)-[:HAS_COMMIT]->(git_commit)
diff --git a/cypher/GitLog/List_git_files_by_resolved_label_and_extension.cypher b/cypher/GitLog/List_git_files_by_resolved_label_and_extension.cypher
new file mode 100644
index 000000000..f333d1f2c
--- /dev/null
+++ b/cypher/GitLog/List_git_files_by_resolved_label_and_extension.cypher
@@ -0,0 +1,14 @@
+// List resolved and unresolved git files by their extension
+
+MATCH (git_file:Git&File)
+OPTIONAL MATCH (git_file)-[:RESOLVES_TO]->(code_file:File&!Git)
+  WITH git_file
+      ,code_file
+      ,(code_file IS NOT NULL)                                      AS resolved
+      ,coalesce(git_file.fileName, git_file.relativePath)           AS gitFileName
+RETURN  resolved
+       ,reverse(split(split(reverse(gitFileName), '/')[0], '.')[0]) AS extension
+       ,count(DISTINCT git_file)                                    AS gitFileCount
+       ,coalesce(labels(code_file), labels(git_file))               AS fileLabels
+       ,collect(DISTINCT gitFileName)[0..9]                         AS gitFileExamples
+ORDER BY resolved ASC, gitFileCount DESC, extension ASC
\ No newline at end of file
diff --git a/cypher/GitLog/Verify_code_to_git_file_unambiguous.cypher b/cypher/GitLog/Verify_code_to_git_file_unambiguous.cypher
new file mode 100644
index 000000000..90fa144ea
--- /dev/null
+++ b/cypher/GitLog/Verify_code_to_git_file_unambiguous.cypher
@@ -0,0 +1,16 @@
+// Verify that code to git file relationships aren't ambiguous
+
+MATCH (git_file:Git&File)-[:RESOLVES_TO]->(code_file:File&!Git)
+ WITH code_file
+     ,count(*)                    AS numberOfResolvedGitFiles
+     ,collect(DISTINCT git_file)  AS git_files
+WHERE numberOfResolvedGitFiles > 1
+UNWIND git_files AS git_file
+OPTIONAL MATCH (git_file)<-[:HAS_FILE]-(git_repository:Git&Repository)
+RETURN numberOfResolvedGitFiles
+      ,collect(DISTINCT coalesce(code_file.absoluteFileName, code_file.fileName))[0..4] AS codeFileExamples
+      ,collect(DISTINCT coalesce(git_file.fileName, git_file.relativePath))[0..4]       AS gitFileExamples
+      ,collect(DISTINCT git_repository.name)[0..4]                                      AS gitRepositoryExamples
+      //,collect(git_repository)[0..9]
+      //,collect(git_file)[0..9]
+      //,collect(code_file)[0..9]
\ No newline at end of file
diff --git a/cypher/GitLog/Verify_git_to_code_file_unambiguous.cypher b/cypher/GitLog/Verify_git_to_code_file_unambiguous.cypher
new file mode 100644
index 000000000..f4c595beb
--- /dev/null
+++ b/cypher/GitLog/Verify_git_to_code_file_unambiguous.cypher
@@ -0,0 +1,17 @@
+// Verify that git to code file relationships aren't ambiguous
+
+MATCH (git_file:Git&File)-[:RESOLVES_TO]->(code_file:File&!Git)
+OPTIONAL MATCH (git_file)<-[:HAS_FILE]-(git_repository:Git&Repository)
+ WITH git_file
+     ,git_repository
+     ,count(*)                    AS numberOfResolvedCodeFiles
+     ,collect(DISTINCT code_file) AS code_files
+WHERE numberOfResolvedCodeFiles > 1
+UNWIND code_files AS code_file
+RETURN numberOfResolvedCodeFiles
+      ,collect(DISTINCT coalesce(code_file.absoluteFileName, code_file.fileName))[0..4] AS codeFileExamples
+      ,collect(DISTINCT coalesce(git_file.fileName, git_file.relativePath))[0..4]       AS gitFileExamples
+      ,collect(DISTINCT git_repository.name)[0..4]                                      AS gitRepositoryExamples
+      //,collect(git_repository)[0..9]
+      //,collect(git_file)[0..9]
+      //,collect(code_file)[0..9]
\ No newline at end of file
diff --git a/scripts/importGit.sh b/scripts/importGit.sh
index 884d30e77..44c19911f 100755
--- a/scripts/importGit.sh
+++ b/scripts/importGit.sh
@@ -124,6 +124,12 @@ commonPostGitImport() {
   echo "importGit: Creating relationships to nodes with matching file names..."
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Add_RESOLVES_TO_relationships_to_git_files_for_Java.cypher"
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Add_RESOLVES_TO_relationships_to_git_files_for_Typescript.cypher"
+
+  # Since it's currently not possible to rule out ambiguity in git<->code file matching,
+  # the following verifications are only an additional info in the log rather than an error.
+  echo "importGit: Running verification queries for troubleshooting (non failing)..."
+  execute_cypher "${GIT_LOG_CYPHER_DIR}/Verify_git_to_code_file_unambiguous.cypher"
+  execute_cypher "${GIT_LOG_CYPHER_DIR}/Verify_code_to_git_file_unambiguous.cypher"
 }
 
 postGitLogImport() {
@@ -147,12 +153,6 @@ postGitPluginImport() {
 
   commonPostGitImport
 
-  #TODO Add verification steps
-  #verificationResult=$( execute_cypher_http_number_of_lines_in_result "${GIT_LOG_CYPHER_DIR}/Verify_code_to_git_file_unambiguous.cypher" )
-  #if [ "${verificationResult}" != 0 ]; then
-  #  echo "importGit: Error: Verification failed. Git:File->!Git:File RESOLVES_TO relationships ambiguous"
-  #fi
-
   echo "importGit: Add numberOfGitCommits property to nodes with matching file names..."
   execute_cypher "${GIT_LOG_CYPHER_DIR}/Set_number_of_git_plugin_commits.cypher"
 }

From 5fd5a69311e16efb555f46a81daead3b0ff4170f Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 17:26:12 +0200
Subject: [PATCH 05/16] Add further Axon Framework artifacts to analyze

---
 scripts/downloader/downloadAxonFramework.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/downloader/downloadAxonFramework.sh b/scripts/downloader/downloadAxonFramework.sh
index 92f437727..00277b43c 100755
--- a/scripts/downloader/downloadAxonFramework.sh
+++ b/scripts/downloader/downloadAxonFramework.sh
@@ -49,6 +49,9 @@ source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axo
 source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axon-messaging" -v "${ARTIFACTS_VERSION}" || exit 2
 source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axon-modelling" -v "${ARTIFACTS_VERSION}" || exit 2
 source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axon-test" -v "${ARTIFACTS_VERSION}" || exit 2
+source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axon-server-connector" -v "${ARTIFACTS_VERSION}" || exit 2
+source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axon-spring-boot-autoconfigure" -v "${ARTIFACTS_VERSION}" || exit 2
+source "${SCRIPTS_DIR}/downloadMavenArtifact.sh" -g "${ARTIFACTS_GROUP}" -a "axon-tracing-opentelemetry" -v "${ARTIFACTS_VERSION}" || exit 2
 
 # Download the git history (bare clone without working tree) into the "source" folder.
 # This makes it possible to additionally import the git log into the graph 

From 81861769474c0136a7f3bafd93b07de2c2ec1b1f Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Thu, 15 Aug 2024 19:58:42 +0200
Subject: [PATCH 06/16] Resolve external modules to internal when file
 extensions match

---
 ...Add_DEPENDS_ON_relationship_to_resolved_modules.cypher | 4 ++--
 ...d_RESOLVES_TO_relationship_for_matching_modules.cypher | 8 +++++---
 cypher/Typescript_Enrichment/Index_module_name.cypher     | 3 +++
 scripts/prepareAnalysis.sh                                | 1 +
 4 files changed, 11 insertions(+), 5 deletions(-)
 create mode 100644 cypher/Typescript_Enrichment/Index_module_name.cypher

diff --git a/cypher/Typescript_Enrichment/Add_DEPENDS_ON_relationship_to_resolved_modules.cypher b/cypher/Typescript_Enrichment/Add_DEPENDS_ON_relationship_to_resolved_modules.cypher
index 8c9c25492..84e304fdb 100644
--- a/cypher/Typescript_Enrichment/Add_DEPENDS_ON_relationship_to_resolved_modules.cypher
+++ b/cypher/Typescript_Enrichment/Add_DEPENDS_ON_relationship_to_resolved_modules.cypher
@@ -6,7 +6,7 @@
  WHERE module <> resolvedModule
   CALL {  WITH module, dependsOn, resolvedModule
          MERGE (module)-[resolvedDependsOn:DEPENDS_ON]->(resolvedModule)
-           SET resolvedDependsOn = dependsOn
-              ,resolvedDependsOn.resolved=true
+            ON CREATE SET resolvedDependsOn          = dependsOn
+                         ,resolvedDependsOn.resolved = true
        } IN TRANSACTIONS
 RETURN count(*) as resolvedDependencies
\ No newline at end of file
diff --git a/cypher/Typescript_Enrichment/Add_RESOLVES_TO_relationship_for_matching_modules.cypher b/cypher/Typescript_Enrichment/Add_RESOLVES_TO_relationship_for_matching_modules.cypher
index e548fc55f..d2cb79bdd 100644
--- a/cypher/Typescript_Enrichment/Add_RESOLVES_TO_relationship_for_matching_modules.cypher
+++ b/cypher/Typescript_Enrichment/Add_RESOLVES_TO_relationship_for_matching_modules.cypher
@@ -8,9 +8,11 @@ WHERE  module.globalFqn IS NOT NULL
 MATCH (externalModule:TS:ExternalModule)
 WHERE module.globalFqn IS NOT NULL
   AND (module.globalFqn = externalModule.globalFqn
-   OR  module.globalFqn = split(externalModule.globalFqn, '/index.')[0]
-   OR  externalModule.globalFqn = split(module.globalFqn, '/index.')[0]
-   OR  (externalModule.name = module.name AND externalModule.namespace = module.namespace)
+   OR   ( externalModule.name              = module.name 
+      AND externalModule.moduleName        = module.moduleName 
+      AND externalModule.namespace         = module.namespace
+      AND externalModule.extensionExtended = module.extensionExtended
+        )
       )
   AND module <> externalModule
  CALL {  WITH module, externalModule
diff --git a/cypher/Typescript_Enrichment/Index_module_name.cypher b/cypher/Typescript_Enrichment/Index_module_name.cypher
new file mode 100644
index 000000000..faff094ba
--- /dev/null
+++ b/cypher/Typescript_Enrichment/Index_module_name.cypher
@@ -0,0 +1,3 @@
+// Create index for module name
+
+CREATE INDEX INDEX_MODULE_NAME IF NOT EXISTS FOR (module:TS) ON (module.moduleName)
\ No newline at end of file
diff --git a/scripts/prepareAnalysis.sh b/scripts/prepareAnalysis.sh
index a654df218..6749599c8 100644
--- a/scripts/prepareAnalysis.sh
+++ b/scripts/prepareAnalysis.sh
@@ -53,6 +53,7 @@ execute_cypher "${CYPHER_DIR}/Create_Typescript_index_for_full_qualified_name.cy
 execute_cypher "${CYPHER_DIR}/Create_Typescript_index_for_name.cypher"
 
 # Preparation - Enrich Graph for Typescript by adding "module" and "name" properties
+execute_cypher "${TYPESCRIPT_CYPHER_DIR}/Index_module_name.cypher"
 execute_cypher "${TYPESCRIPT_CYPHER_DIR}/Add_module_properties.cypher"
 
 # Preparation - Enrich Graph for Typescript by adding a name properties

From 3a0ff20fa1828cc1788dd643ac60bd756339d64c Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Thu, 15 Aug 2024 21:38:37 +0200
Subject: [PATCH 07/16] Add progress and improve performance of change
 detection

---
 scripts/detectChangedArtifacts.sh | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/scripts/detectChangedArtifacts.sh b/scripts/detectChangedArtifacts.sh
index 15b7d9d66..22d7b550b 100755
--- a/scripts/detectChangedArtifacts.sh
+++ b/scripts/detectChangedArtifacts.sh
@@ -70,7 +70,7 @@ get_file_size() {
 }
 
 # Function to process a single path
-unwind_directories() {
+file_names_and_sizes() {
     if [ -d "$1" ]; then
         # If it's a directory, list all files inside 
         # except for "node_modules", "target", "temp" and the change detection file itself
@@ -80,10 +80,11 @@ unwind_directories() {
           -type d -name "temp" -prune -o \
           -not -name "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE}" \
           -type f \
+          -exec stat -f "%N %z" {} + \
         | sort 
     elif [ -f "$1" ]; then
         # If it's a file, just echo the file path
-        echo "$1"
+        stat -f "%N %z" < "$1"
     fi
 }
 
@@ -92,17 +93,18 @@ unwind_directories() {
 # and calculates the md5 hash for every of these .
 get_md5_checksum_of_all_file_names_and_sizes() {
   local paths=${1}
-  local files_and_sizes=""
+  local total_paths; total_paths=$(echo "${paths}" | awk -F '[\t,]' '{print NF}')
+  local all_files_and_sizes=""
+  local processed_paths=0
 
   for path in ${paths//,/ }; do
-      files=$(unwind_directories "${path}")
-      for file in ${files}; do
-          size=$(get_file_size "${file}")
-          files_and_sizes="${files_and_sizes}${file}${size}"
-      done
+      local files_and_their_size; files_and_their_size=$(file_names_and_sizes "${path}")
+      all_files_and_sizes="${all_files_and_sizes}${files_and_their_size}"
+      processed_paths=$((processed_paths + 1))
+      echo -ne "detectChangedArtifacts: Calculate checksum progress: ($processed_paths/$total_paths)\r" >&2
   done
-
-  echo "${files_and_sizes}" | openssl md5 | awk '{print $2}'
+  echo "" >&2
+  echo "${all_files_and_sizes}" | openssl md5 | awk '{print $2}'
 }
 
 # Use find to list all files in the directory with their properties,
@@ -118,6 +120,8 @@ if [ ! -f "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}" ] ; then
         mkdir -p "${ARTIFACTS_DIRECTORY}"
         echo "${CURRENT_ARTIFACTS_HASH}" > "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}"
         echo "detectChangedArtifacts: Change detection file created" >&2
+    else
+        echo "detectChangedArtifacts: Skipping file creation with content (=hash) ${CURRENT_ARTIFACTS_HASH}" >&2
     fi
     echo 1 # 1=Change detected and change detection file created
     exit 0
@@ -132,6 +136,8 @@ else
         # Write the updated hash into the file containing the hash of the files list for the next call
         echo "$CURRENT_ARTIFACTS_HASH" > "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}"
         echo "detectChangedArtifacts: Change detection file updated" >&2
+    else
+        echo "detectChangedArtifacts: Skipping file update with content (=hash) ${CURRENT_ARTIFACTS_HASH}" >&2
     fi
     echo 2 # 2=Change detected and change detection file updated
 fi
\ No newline at end of file

From 6da4f8379891dae7effcf1aef214be9ef31620c5 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Fri, 16 Aug 2024 20:51:48 +0200
Subject: [PATCH 08/16] Improve performance by only searching relevant paths

---
 scripts/findPathsToScan.sh | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/scripts/findPathsToScan.sh b/scripts/findPathsToScan.sh
index bd1bf97d5..9b1bc7641 100755
--- a/scripts/findPathsToScan.sh
+++ b/scripts/findPathsToScan.sh
@@ -45,11 +45,17 @@ if [ -d "./${SOURCE_DIRECTORY}" ] ; then
         echo "findPathsToScan: Scanning Typescript source using @jqassistant/ts-lce..." >&2
         ( cd "./${SOURCE_DIRECTORY}" && npx --yes @jqassistant/ts-lce@1.2.1 --extension React >"./../runtime/logs/jqassistant-typescript-scan.log" 2>&1 || exit )
     else
-        echo "findPathToScan Error: Command npx not found. It's needed to execute @jqassistant/ts-lce to scan Typescript projects."
+        echo "findPathToScan Error: Command npx not found. It's needed to execute @jqassistant/ts-lce to scan Typescript projects." >&2
     fi
 
     # Scan Typescript analysis json data files in the source directory
-    typescriptAnalysisFiles="$(find "./${SOURCE_DIRECTORY}" -type f -path "*/.reports/jqa/ts-output.json" -exec echo typescript:project::{} \; | tr '\n' ',' | sed 's/,$/\n/')"
+    typescriptAnalysisFiles="$(find "./${SOURCE_DIRECTORY}" \
+                                    -type d -name "node_modules" -prune -o \
+                                    -type d -name "target" -prune -o \
+                                    -type d -name "temp" -prune -o \
+                                    -type f -path "*/.reports/jqa/ts-output.json" \
+                                    -exec echo typescript:project::{} \; | tr '\n' ',' | sed 's/,$/\n/')"
+
     if [ -n "${typescriptAnalysisFiles}" ]; then
         directoriesAndFilesToScan="$(appendNonEmpty "${directoriesAndFilesToScan}")${typescriptAnalysisFiles}"
     fi
@@ -64,7 +70,11 @@ if [ -d "./${SOURCE_DIRECTORY}" ] ; then
 
     # Scan git repositories in the artifacts directory
     if [ "${IMPORT_GIT_LOG_DATA_IF_SOURCE_IS_PRESENT}" = "" ] || [ "${IMPORT_GIT_LOG_DATA_IF_SOURCE_IS_PRESENT}" = "plugin" ] ; then
-        gitDirectories="$(find "./${SOURCE_DIRECTORY}" -type d -name ".git" -exec echo {} \; | tr '\n' ',' | sed 's/,$/\n/')"
+        gitDirectories="$(find "./${SOURCE_DIRECTORY}" \
+                                -type d -name "node_modules" -prune -o \
+                                -type d -name "target" -prune -o \
+                                -type d -name "temp" -prune -o \
+                                -type d -name ".git" -exec echo {} \; | tr '\n' ',' | sed 's/,$/\n/')"
         if [ -n "${gitDirectories}" ]; then
             directoriesAndFilesToScan="$(appendNonEmpty "${directoriesAndFilesToScan}")${gitDirectories}"
         fi

From 20ffe20eaafe82c8c9315271be2c2b3528bfc51d Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Fri, 16 Aug 2024 21:13:02 +0200
Subject: [PATCH 09/16] Copy Typescript scanning log to console and file

---
 scripts/findPathsToScan.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/scripts/findPathsToScan.sh b/scripts/findPathsToScan.sh
index 9b1bc7641..1830891a1 100755
--- a/scripts/findPathsToScan.sh
+++ b/scripts/findPathsToScan.sh
@@ -43,7 +43,13 @@ if [ -d "./${SOURCE_DIRECTORY}" ] ; then
         # TODO: Remove patchJQAssistantTypescriptPlugin when issue is resolved: https://github.com/jqassistant-plugin/jqassistant-typescript-plugin/issues/125
         source "${SCRIPTS_DIR}/patchJQAssistantTypescriptPlugin.sh" >&2
         echo "findPathsToScan: Scanning Typescript source using @jqassistant/ts-lce..." >&2
-        ( cd "./${SOURCE_DIRECTORY}" && npx --yes @jqassistant/ts-lce@1.2.1 --extension React >"./../runtime/logs/jqassistant-typescript-scan.log" 2>&1 || exit )
+        # Note: The npx command will be executed in the source directory using a subshell by putting parentheses around it.
+        #       The subshell is the reason why it isn't needed to change back to the main directory after execution.
+        # Note: This script must not output anything except for the return code to stdout,
+        #       all output of the scanning needs to be redirected to stderr using ">&2".
+        #       For later troubleshooting, the output is also copied to a dedicated log file using "tee".
+        # Note: Don't worry about the hardcoded version number. It will be updated by Renovate using a custom Manager.
+        ( cd "./${SOURCE_DIRECTORY}" && npx --yes @jqassistant/ts-lce@1.2.1 --extension React 2>&1 | tee "./../runtime/logs/jqassistant-typescript-scan.log" >&2 || exit )
     else
         echo "findPathToScan Error: Command npx not found. It's needed to execute @jqassistant/ts-lce to scan Typescript projects." >&2
     fi

From 7c03d491d91a9b407d138be89afcddb01ecea9a2 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sat, 17 Aug 2024 20:53:04 +0200
Subject: [PATCH 10/16] Add data verification before projection creation.

---
 .../Dependencies_0_Verify_Projectable.cypher  | 33 +++++++++++
 scripts/projectionFunctions.sh                | 57 ++++++++++++++++++-
 2 files changed, 88 insertions(+), 2 deletions(-)
 create mode 100644 cypher/Dependencies_Projection/Dependencies_0_Verify_Projectable.cypher

diff --git a/cypher/Dependencies_Projection/Dependencies_0_Verify_Projectable.cypher b/cypher/Dependencies_Projection/Dependencies_0_Verify_Projectable.cypher
new file mode 100644
index 000000000..43523cfec
--- /dev/null
+++ b/cypher/Dependencies_Projection/Dependencies_0_Verify_Projectable.cypher
@@ -0,0 +1,33 @@
+// Verify that nodes and relationships are complete and ready for projection
+
+ MATCH (source:TS:Module)-[dependency:DEPENDS_ON]->(target:Module)
+ WHERE $dependencies_projection_node            IN labels(source)
+   AND $dependencies_projection_node            IN labels(target)
+  WITH (NOT $dependencies_projection_weight_property IN keys(dependency)) AS missingWeightProperty
+      ,(dependency[$dependencies_projection_weight_property])             AS weightPropertyValue
+      ,(dependency[$dependencies_projection_weight_property] < 1)         AS nonPositiveWeightPropertyValue
+      ,coalesce(dependency.resolved, false)                               AS resolvedDependency
+      ,EXISTS { (target)<-[:RESOLVES_TO]-(resolvedTarget:ExternalModule) } AS resolvedTarget
+      ,(source.incomingDependencies IS NULL OR
+        target.incomingDependencies IS NULL)   AS missingIncomingDependencies
+      ,(source.outgoingDependencies IS NULL OR 
+        target.outgoingDependencies IS NULL)   AS missingOutgoingDependencies
+      ,source
+      ,target
+ WHERE missingWeightProperty
+//    OR nonPositiveWeightPropertyValue // if strict positive weights are needed 
+    OR missingIncomingDependencies
+    OR missingOutgoingDependencies
+RETURN missingWeightProperty
+      ,nonPositiveWeightPropertyValue
+      ,resolvedDependency
+      ,resolvedTarget
+      ,missingIncomingDependencies
+      ,missingOutgoingDependencies
+      ,count(*) AS numberOfRelationships
+      ,min(weightPropertyValue) AS minWeightPropertyValue
+      ,max(weightPropertyValue) AS maxWeightPropertyValue
+      ,collect(DISTINCT source.globalFqn + ' -> ' + target.globalFqn)[0..4] AS examples
+      // Output source and target nodes for troubleshooting
+      //,collect(source)[0..4]
+      //,collect(target)[0..4]
\ No newline at end of file
diff --git a/scripts/projectionFunctions.sh b/scripts/projectionFunctions.sh
index 2f5106170..8403b9230 100644
--- a/scripts/projectionFunctions.sh
+++ b/scripts/projectionFunctions.sh
@@ -64,6 +64,54 @@ logNoDataForProjection() {
     echo "projectionFunctions: $(date +'%Y-%m-%dT%H:%M:%S%z') No data. ${programmingLanguage} ${projectionName} analysis skipped."
 }
 
+# Writes a log entry for the case when data validation failed.
+#
+# Required Parameters:
+# - dependencies_projection=...
+#   Name prefix for the in-memory projection name for dependencies. Example: "type-centrality"
+# - dependencies_projection_language=...
+#   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
+# - verificationResult=...
+#   Full query result of the failed verification
+logDataVerificationFailedForProjection() {
+    local programmingLanguage projectionName verificationResult
+    programmingLanguage=$( extractQueryParameter "dependencies_projection_language" "${@}" )
+    programmingLanguage=${programmingLanguage:-"Java"} # Set to default value "Java" if not set since it is optional
+    projectionName=$( extractQueryParameter "dependencies_projection" "${@}" )
+    redColor='\033[0;31m'
+    noColor='\033[0m'
+    echo -e "${redColor}projectionFunctions: $(date +'%Y-%m-%dT%H:%M:%S%z') Error. Data validation for ${programmingLanguage} ${projectionName} failed.${noColor}" >&2
+    echo -e "${redColor}  -> This might be due to missing node or relationship properties.${noColor}" >&2
+    echo -e "${redColor}     For more details see the following verification query and its result (CSV):${noColor}" >&2
+}
+
+# Verifies if the nodes and relationships properties are complete (no missing properties) and the data is ready for projection.
+#
+# Returns true  (=0) if the data is ready for projection.
+# Returns false (=1) if the verification failed.
+# Exits with an error if there are technical issues.
+#
+# Required Parameters:
+# - dependencies_projection=...
+#   Name prefix for the in-memory projection name for dependencies. Example: "type-centrality"
+# - dependencies_projection_node=...
+#   Label of the nodes that will be used for the projection. Example: "Type"
+# - dependencies_projection_weight_property=...
+#   Name of the node property that contains the dependency weight. Example: "weight"
+# - dependencies_projection_language=...
+#   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
+verifyDataReadyForProjection() {
+    local verificationResult
+    verificationResult=$( execute_cypher "${PROJECTION_CYPHER_DIR}/Dependencies_0_Verify_Projectable.cypher" "${@}")
+    if is_csv_column_greater_zero "${verificationResult}" "numberOfRelationships"; then
+        logDataVerificationFailedForProjection "${@}" "verificationResult=${verificationResult}"
+        redColor='\033[0;31m'
+        noColor='\033[0m'
+        echo -e "${redColor}${verificationResult}${noColor}" >&2
+        exit 1;
+    fi
+}
+
 # Creates a directed Graph projection for dependencies between nodes specified by the parameter "dependencies_projection_node".
 # Nodes without incoming and outgoing dependencies will be filtered out using a subgraph.
 #
@@ -82,9 +130,10 @@ logNoDataForProjection() {
 #   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
 createDirectedDependencyProjection() {
     logProjectionCreationStart "${@}"
+    verifyDataReadyForProjection "${@}"
 
     projectionCheckResult=$( execute_cypher_http_number_of_lines_in_result "${PROJECTION_CYPHER_DIR}/Dependencies_0_Check_Projectable.cypher" "${@}" )
-    if [[ "${projectionCheckResult}" -lt 1 ]]; then
+    if [ "${projectionCheckResult}" -lt 1 ]; then
         logNoDataForProjection "${@}"
         return 1
     fi
@@ -120,9 +169,10 @@ createDirectedDependencyProjection() {
 #   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
 createUndirectedDependencyProjection() {
     logProjectionCreationStart "${@}"
+    verifyDataReadyForProjection "${@}"
 
     projectionCheckResult=$( execute_cypher_http_number_of_lines_in_result "${PROJECTION_CYPHER_DIR}/Dependencies_0_Check_Projectable.cypher" "${@}" )
-    if [[ "${projectionCheckResult}" -lt 1 ]]; then
+    if [ "${projectionCheckResult}" -lt 1 ]; then
         return 1
     fi
     execute_cypher "${PROJECTION_CYPHER_DIR}/Dependencies_1_Delete_Projection.cypher" "${@}" >/dev/null
@@ -153,6 +203,7 @@ createUndirectedDependencyProjection() {
 #   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
 createDirectedJavaTypeDependencyProjection() {
     logProjectionCreationStart "${@}"
+    verifyDataReadyForProjection "${@}" "dependencies_projection_node=Type" "dependencies_projection_weight_property=weight"
 
     execute_cypher "${PROJECTION_CYPHER_DIR}/Dependencies_2_Delete_Subgraph.cypher" "${@}" >/dev/null
     
@@ -180,6 +231,7 @@ createDirectedJavaTypeDependencyProjection() {
 #   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
 createUndirectedJavaTypeDependencyProjection() {
     logProjectionCreationStart "${@}"
+    verifyDataReadyForProjection "${@}" "dependencies_projection_node=Type" "dependencies_projection_weight_property=weight"
 
     execute_cypher "${PROJECTION_CYPHER_DIR}/Dependencies_2_Delete_Subgraph.cypher" "${@}" >/dev/null
 
@@ -207,6 +259,7 @@ createUndirectedJavaTypeDependencyProjection() {
 #   Optional name of the associated programming language for logging details. Default: "Java". Example: "Typescript"
 createDirectedJavaMethodDependencyProjection() {
     logProjectionCreationStart "${@}"
+    verifyDataReadyForProjection "${@}" "dependencies_projection_node=Method" "dependencies_projection_weight_property=weight"
 
     execute_cypher "${PROJECTION_CYPHER_DIR}/Dependencies_2_Delete_Subgraph.cypher" "${@}" >/dev/null
 

From 4333805ad3b222b529e5a794ba244c3928831940 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 08:14:11 +0200
Subject: [PATCH 11/16] Rename to more general detectChangedFiles

---
 ...ngedArtifacts.sh => detectChangedFiles.sh} | 41 +++++++++++--------
 scripts/resetAndScanChanged.sh                |  8 ++--
 2 files changed, 27 insertions(+), 22 deletions(-)
 rename scripts/{detectChangedArtifacts.sh => detectChangedFiles.sh} (69%)

diff --git a/scripts/detectChangedArtifacts.sh b/scripts/detectChangedFiles.sh
similarity index 69%
rename from scripts/detectChangedArtifacts.sh
rename to scripts/detectChangedFiles.sh
index 22d7b550b..68a45a8cd 100755
--- a/scripts/detectChangedArtifacts.sh
+++ b/scripts/detectChangedFiles.sh
@@ -16,12 +16,13 @@ set -o errexit -o pipefail
 
 # Overrideable defaults
 ARTIFACTS_DIRECTORY=${ARTIFACTS_DIRECTORY:-"artifacts"}
-ARTIFACTS_CHANGE_DETECTION_HASH_FILE=${ARTIFACTS_CHANGE_DETECTION_HASH_FILE:-"artifactsChangeDetectionHash.txt"} # Name of the file that contains the hash code of the file list for change detection
-ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH="./${ARTIFACTS_DIRECTORY}/$ARTIFACTS_CHANGE_DETECTION_HASH_FILE"
+ARTIFACTS_CHANGE_DETECTION_HASH_FILE=${ARTIFACTS_CHANGE_DETECTION_HASH_FILE:-"artifactsChangeDetectionHash.txt"} # !DEPRECATED! Use CHANGE_DETECTION_HASH_FILE.
+CHANGE_DETECTION_HASH_FILE=${CHANGE_DETECTION_HASH_FILE:-"${ARTIFACTS_CHANGE_DETECTION_HASH_FILE}"} # Name of the file that contains the hash code of the file list for change detection
+CHANGE_DETECTION_HASH_FILE_PATH=${CHANGE_DETECTION_HASH_FILE_PATH:-"./${ARTIFACTS_DIRECTORY}/${CHANGE_DETECTION_HASH_FILE}"} # Path of the file that contains the hash code of the file list for change detection
 
 # Function to display script usage
 usage() {
-  echo "Usage: $0 [--readonly] [--paths <comma separated list of file and directory names>]"
+  echo "Usage: $0 [--readonly] [--paths <comma separated list of file and directory names> (default=artifacts)]"
   exit 1
 }
 
@@ -43,7 +44,7 @@ while [[ $# -gt 0 ]]; do
       shift
       ;;
     *)
-      echo "detectChangedArtifacts: Error: Unknown option: ${key}"
+      echo "detectChangedFiles: Error: Unknown option: ${key}"
       usage
       ;;
   esac
@@ -51,10 +52,12 @@ while [[ $# -gt 0 ]]; do
 done
 
 if ${readonlyMode}; then
-  echo "detectChangedArtifacts: Readonly mode activated. Change detection file won't be created." >&2
+  echo "detectChangedFiles: Readonly mode activated. Change detection file won't be created." >&2
+else
+  echo "detectChangedFiles: ${CHANGE_DETECTION_HASH_FILE_PATH} will be used as change detection file." >&2
 fi
 
-# Check if the artifacts directory exists
+# Check if the paths parameter exist
 if [ -z "${paths}" ] ; then
     echo 0 # 0=No change detected. The path list is empty. There is nothing to compare. Therefore assume that there are no changes.
     exit 0
@@ -78,7 +81,7 @@ file_names_and_sizes() {
           -type d -name "node_modules" -prune -o \
           -type d -name "target" -prune -o \
           -type d -name "temp" -prune -o \
-          -not -name "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE}" \
+          -not -path "${CHANGE_DETECTION_HASH_FILE_PATH}" \
           -type f \
           -exec stat -f "%N %z" {} + \
         | sort 
@@ -101,7 +104,7 @@ get_md5_checksum_of_all_file_names_and_sizes() {
       local files_and_their_size; files_and_their_size=$(file_names_and_sizes "${path}")
       all_files_and_sizes="${all_files_and_sizes}${files_and_their_size}"
       processed_paths=$((processed_paths + 1))
-      echo -ne "detectChangedArtifacts: Calculate checksum progress: ($processed_paths/$total_paths)\r" >&2
+      echo -ne "detectChangedFiles: Calculate checksum progress: ($processed_paths/$total_paths)\r" >&2
   done
   echo "" >&2
   echo "${all_files_and_sizes}" | openssl md5 | awk '{print $2}'
@@ -111,17 +114,19 @@ get_md5_checksum_of_all_file_names_and_sizes() {
 # sort the output, and pipe it to md5 to create a hash
 # Use openssl md5 that is at least available on Mac and Linux. 
 # See: https://github.com/TRON-US/go-btfs/issues/90#issuecomment-517409369
-CURRENT_ARTIFACTS_HASH=$(get_md5_checksum_of_all_file_names_and_sizes "${paths}")
+CURRENT_FILES_HASH=$(get_md5_checksum_of_all_file_names_and_sizes "${paths}")
 
 # Assume that the files where changed if the file containing the hash of the file list does not exist yet.
-if [ ! -f "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}" ] ; then
+if [ ! -f "${CHANGE_DETECTION_HASH_FILE_PATH}" ] ; then
     if [ "${readonlyMode}" = false ] ; then
+        # Create the directory for the hash file if it hadn't existed yet.
+        hash_file_directory=$(dirname "${CHANGE_DETECTION_HASH_FILE_PATH}")
+        mkdir -p "${hash_file_directory}"
         # Create the file containing the hash of the files list to a new file for the next call
-        mkdir -p "${ARTIFACTS_DIRECTORY}"
-        echo "${CURRENT_ARTIFACTS_HASH}" > "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}"
-        echo "detectChangedArtifacts: Change detection file created" >&2
+        echo "${CURRENT_FILES_HASH}" > "${CHANGE_DETECTION_HASH_FILE_PATH}"
+        echo "detectChangedFiles: Change detection file created" >&2
     else
-        echo "detectChangedArtifacts: Skipping file creation with content (=hash) ${CURRENT_ARTIFACTS_HASH}" >&2
+        echo "detectChangedFiles: Skipping file creation with content (=hash) ${CURRENT_FILES_HASH}" >&2
     fi
     echo 1 # 1=Change detected and change detection file created
     exit 0
@@ -129,15 +134,15 @@ fi
 
 # Assume that there is no change if the saved hash is equal to the current one.
 # Otherwise assume that the files where changed and overwrite the hash with the current one for the next call
-if [[ $(< "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}") == "$CURRENT_ARTIFACTS_HASH" ]] ; then
+if [[ $(< "${CHANGE_DETECTION_HASH_FILE_PATH}") == "$CURRENT_FILES_HASH" ]] ; then
     echo 0 # 0=No change detected
 else
     if ! ${readonlyMode}; then
         # Write the updated hash into the file containing the hash of the files list for the next call
-        echo "$CURRENT_ARTIFACTS_HASH" > "${ARTIFACTS_CHANGE_DETECTION_HASH_FILE_PATH}"
-        echo "detectChangedArtifacts: Change detection file updated" >&2
+        echo "$CURRENT_FILES_HASH" > "${CHANGE_DETECTION_HASH_FILE_PATH}"
+        echo "detectChangedFiles: Change detection file updated" >&2
     else
-        echo "detectChangedArtifacts: Skipping file update with content (=hash) ${CURRENT_ARTIFACTS_HASH}" >&2
+        echo "detectChangedFiles: Skipping file update with content (=hash) ${CURRENT_FILES_HASH}" >&2
     fi
     echo 2 # 2=Change detected and change detection file updated
 fi
\ No newline at end of file
diff --git a/scripts/resetAndScanChanged.sh b/scripts/resetAndScanChanged.sh
index 04a69a3e0..43c409e7a 100755
--- a/scripts/resetAndScanChanged.sh
+++ b/scripts/resetAndScanChanged.sh
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash
 
-# Executes "resetAndScan.sh" only if "detectChangedArtifacts.sh" returns detected changes.
+# Executes "resetAndScan.sh" only if "detectChangedFiles.sh" returns detected changes.
 
 # Note: "resetAndScan" expects jQAssistant to be installed in the "tools" directory.
 
-# Requires resetAndScan.sh, copyPackageJsonFiles.sh, detectChangedArtifacts.sh, findPathsToScan.sh
+# Requires resetAndScan.sh, copyPackageJsonFiles.sh, detectChangedFiles.sh, findPathsToScan.sh
 
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -o errexit -o pipefail
@@ -24,11 +24,11 @@ filesAndDirectoriesToScan=$( source "${SCRIPTS_DIR}/findPathsToScan.sh" )
 source "${SCRIPTS_DIR}/copyPackageJsonFiles.sh"
 
 # Scan and analyze Artifacts when they were changed
-changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedArtifacts.sh" --readonly --paths "${filesAndDirectoriesToScan}")
+changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedFiles.sh" --readonly --paths "${filesAndDirectoriesToScan}")
 if [[ "${changeDetectionReturnCode}" == "0" ]] ; then
     echo "resetAndScanChanged: Artifacts unchanged. Scan skipped."
 else
     echo "resetAndScanChanged: Detected change (${changeDetectionReturnCode}). Resetting database and scanning artifacts."
     source "${SCRIPTS_DIR}/resetAndScan.sh" "${filesAndDirectoriesToScan}"
-    changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedArtifacts.sh" --paths "${filesAndDirectoriesToScan}")
+    changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedFiles.sh" --paths "${filesAndDirectoriesToScan}")
 fi
\ No newline at end of file

From c0e290d2676f8d83a7414ac1f7ba6a49e05a08b0 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 11:20:57 +0200
Subject: [PATCH 12/16] Add custom hashfile path option to change detection

---
 scripts/detectChangedFiles.sh | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/scripts/detectChangedFiles.sh b/scripts/detectChangedFiles.sh
index 68a45a8cd..4193c5252 100755
--- a/scripts/detectChangedFiles.sh
+++ b/scripts/detectChangedFiles.sh
@@ -18,17 +18,20 @@ set -o errexit -o pipefail
 ARTIFACTS_DIRECTORY=${ARTIFACTS_DIRECTORY:-"artifacts"}
 ARTIFACTS_CHANGE_DETECTION_HASH_FILE=${ARTIFACTS_CHANGE_DETECTION_HASH_FILE:-"artifactsChangeDetectionHash.txt"} # !DEPRECATED! Use CHANGE_DETECTION_HASH_FILE.
 CHANGE_DETECTION_HASH_FILE=${CHANGE_DETECTION_HASH_FILE:-"${ARTIFACTS_CHANGE_DETECTION_HASH_FILE}"} # Name of the file that contains the hash code of the file list for change detection
-CHANGE_DETECTION_HASH_FILE_PATH=${CHANGE_DETECTION_HASH_FILE_PATH:-"./${ARTIFACTS_DIRECTORY}/${CHANGE_DETECTION_HASH_FILE}"} # Path of the file that contains the hash code of the file list for change detection
+CHANGE_DETECTION_HASH_FILE_PATH=${CHANGE_DETECTION_HASH_FILE_PATH:-"./${ARTIFACTS_DIRECTORY}/${CHANGE_DETECTION_HASH_FILE}"} # Default path of the file that contains the hash code of the file list for change detection. Can be overridden by a command line option.
 
 # Function to display script usage
 usage() {
-  echo "Usage: $0 [--readonly] [--paths <comma separated list of file and directory names> (default=artifacts)]"
+  echo "Usage: $0 [--readonly]"
+  echo "          [--paths <comma separated list of file and directory names> (default=artifacts)]"
+  echo "          [--hashfile <path to the file that contains the hash for change detection> (default=env var CHANGE_DETECTION_HASH_FILE_PATH)]"
   exit 1
 }
 
 # Default values
 readonlyMode=false
 paths="./${ARTIFACTS_DIRECTORY}"
+hashFilePath="${CHANGE_DETECTION_HASH_FILE_PATH}"
 
 # Parse command line arguments
 while [[ $# -gt 0 ]]; do
@@ -43,6 +46,10 @@ while [[ $# -gt 0 ]]; do
       paths="${value}"
       shift
       ;;
+    --hashfile)
+      hashFilePath="${value}"
+      shift
+      ;;
     *)
       echo "detectChangedFiles: Error: Unknown option: ${key}"
       usage
@@ -54,7 +61,7 @@ done
 if ${readonlyMode}; then
   echo "detectChangedFiles: Readonly mode activated. Change detection file won't be created." >&2
 else
-  echo "detectChangedFiles: ${CHANGE_DETECTION_HASH_FILE_PATH} will be used as change detection file." >&2
+  echo "detectChangedFiles: ${hashFilePath} will be used as change detection file." >&2
 fi
 
 # Check if the paths parameter exist
@@ -81,7 +88,7 @@ file_names_and_sizes() {
           -type d -name "node_modules" -prune -o \
           -type d -name "target" -prune -o \
           -type d -name "temp" -prune -o \
-          -not -path "${CHANGE_DETECTION_HASH_FILE_PATH}" \
+          -not -path "${hashFilePath}" \
           -type f \
           -exec stat -f "%N %z" {} + \
         | sort 
@@ -117,13 +124,13 @@ get_md5_checksum_of_all_file_names_and_sizes() {
 CURRENT_FILES_HASH=$(get_md5_checksum_of_all_file_names_and_sizes "${paths}")
 
 # Assume that the files where changed if the file containing the hash of the file list does not exist yet.
-if [ ! -f "${CHANGE_DETECTION_HASH_FILE_PATH}" ] ; then
+if [ ! -f "${hashFilePath}" ] ; then
     if [ "${readonlyMode}" = false ] ; then
         # Create the directory for the hash file if it hadn't existed yet.
-        hash_file_directory=$(dirname "${CHANGE_DETECTION_HASH_FILE_PATH}")
+        hash_file_directory=$(dirname "${hashFilePath}")
         mkdir -p "${hash_file_directory}"
         # Create the file containing the hash of the files list to a new file for the next call
-        echo "${CURRENT_FILES_HASH}" > "${CHANGE_DETECTION_HASH_FILE_PATH}"
+        echo "${CURRENT_FILES_HASH}" > "${hashFilePath}"
         echo "detectChangedFiles: Change detection file created" >&2
     else
         echo "detectChangedFiles: Skipping file creation with content (=hash) ${CURRENT_FILES_HASH}" >&2
@@ -134,12 +141,12 @@ fi
 
 # Assume that there is no change if the saved hash is equal to the current one.
 # Otherwise assume that the files where changed and overwrite the hash with the current one for the next call
-if [[ $(< "${CHANGE_DETECTION_HASH_FILE_PATH}") == "$CURRENT_FILES_HASH" ]] ; then
+if [[ $(< "${hashFilePath}") == "${CURRENT_FILES_HASH}" ]] ; then
     echo 0 # 0=No change detected
 else
     if ! ${readonlyMode}; then
         # Write the updated hash into the file containing the hash of the files list for the next call
-        echo "$CURRENT_FILES_HASH" > "${CHANGE_DETECTION_HASH_FILE_PATH}"
+        echo "${CURRENT_FILES_HASH}" > "${hashFilePath}"
         echo "detectChangedFiles: Change detection file updated" >&2
     else
         echo "detectChangedFiles: Skipping file update with content (=hash) ${CURRENT_FILES_HASH}" >&2

From d1f035345f5ed41157dc974cd55b5007a9124163 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 11:21:54 +0200
Subject: [PATCH 13/16] Scan Typescript sources only on changes.

---
 README.md                      |  1 +
 scripts/findPathsToScan.sh     | 15 ----------
 scripts/resetAndScanChanged.sh |  7 +++--
 scripts/scanTypescript.sh      | 53 ++++++++++++++++++++++++++++++++++
 4 files changed, 58 insertions(+), 18 deletions(-)
 create mode 100755 scripts/scanTypescript.sh

diff --git a/README.md b/README.md
index a057a56d9..2be3e9960 100644
--- a/README.md
+++ b/README.md
@@ -182,6 +182,7 @@ The [Code Structure Analysis Pipeline](./.github/workflows/java-code-analysis.ym
 
 - How can i trigger a full re-scan of all artifacts?  
   👉 Delete the file `artifactsChangeDetectionHash.txt` in the `artifacts` directory.
+  👉 Delete the file `typescriptFileChangeDetectionHashFile.txt` in the `source` directory to additionally re-scan Typescript projects.
 
 - How can i enable PDF generation for Jupyter Notebooks (depends on chromium, takes more time)?  
   👉 Set environment variable `ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION` to anything except an empty string. Example:  
diff --git a/scripts/findPathsToScan.sh b/scripts/findPathsToScan.sh
index 1830891a1..0af6f2515 100755
--- a/scripts/findPathsToScan.sh
+++ b/scripts/findPathsToScan.sh
@@ -39,21 +39,6 @@ else
 fi
 
 if [ -d "./${SOURCE_DIRECTORY}" ] ; then
-    if command -v "npx" &> /dev/null ; then
-        # TODO: Remove patchJQAssistantTypescriptPlugin when issue is resolved: https://github.com/jqassistant-plugin/jqassistant-typescript-plugin/issues/125
-        source "${SCRIPTS_DIR}/patchJQAssistantTypescriptPlugin.sh" >&2
-        echo "findPathsToScan: Scanning Typescript source using @jqassistant/ts-lce..." >&2
-        # Note: The npx command will be executed in the source directory using a subshell by putting parentheses around it.
-        #       The subshell is the reason why it isn't needed to change back to the main directory after execution.
-        # Note: This script must not output anything except for the return code to stdout,
-        #       all output of the scanning needs to be redirected to stderr using ">&2".
-        #       For later troubleshooting, the output is also copied to a dedicated log file using "tee".
-        # Note: Don't worry about the hardcoded version number. It will be updated by Renovate using a custom Manager.
-        ( cd "./${SOURCE_DIRECTORY}" && npx --yes @jqassistant/ts-lce@1.2.1 --extension React 2>&1 | tee "./../runtime/logs/jqassistant-typescript-scan.log" >&2 || exit )
-    else
-        echo "findPathToScan Error: Command npx not found. It's needed to execute @jqassistant/ts-lce to scan Typescript projects." >&2
-    fi
-
     # Scan Typescript analysis json data files in the source directory
     typescriptAnalysisFiles="$(find "./${SOURCE_DIRECTORY}" \
                                     -type d -name "node_modules" -prune -o \
diff --git a/scripts/resetAndScanChanged.sh b/scripts/resetAndScanChanged.sh
index 43c409e7a..5abd5d758 100755
--- a/scripts/resetAndScanChanged.sh
+++ b/scripts/resetAndScanChanged.sh
@@ -4,7 +4,7 @@
 
 # Note: "resetAndScan" expects jQAssistant to be installed in the "tools" directory.
 
-# Requires resetAndScan.sh, copyPackageJsonFiles.sh, detectChangedFiles.sh, findPathsToScan.sh
+# Requires resetAndScan.sh, copyPackageJsonFiles.sh, scanTypescript.sh, detectChangedFiles.sh, findPathsToScan.sh
 
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -o errexit -o pipefail
@@ -16,12 +16,13 @@ set -o errexit -o pipefail
 SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
 echo "resetAndScanChanged SCRIPTS_DIR=${SCRIPTS_DIR}"
 
-filesAndDirectoriesToScan=$( source "${SCRIPTS_DIR}/findPathsToScan.sh" )
-
 # Prepare scan
 # TODO "copyPackageJsonFiles.sh" can be deleted here when the following issue is resolved:
 # https://github.com/jqassistant-plugin/jqassistant-npm-plugin/issues/5
 source "${SCRIPTS_DIR}/copyPackageJsonFiles.sh"
+source "${SCRIPTS_DIR}/scanTypescript.sh"
+
+filesAndDirectoriesToScan=$( source "${SCRIPTS_DIR}/findPathsToScan.sh" )
 
 # Scan and analyze Artifacts when they were changed
 changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedFiles.sh" --readonly --paths "${filesAndDirectoriesToScan}")
diff --git a/scripts/scanTypescript.sh b/scripts/scanTypescript.sh
new file mode 100755
index 000000000..431e278c4
--- /dev/null
+++ b/scripts/scanTypescript.sh
@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+
+# Executes the npm package @jqassistant/ts-lc using npx to scan the Typescript projects in the source directory and create an intermediate json data file for the jQAssistant Typescript plugin.
+
+# Uses: patchJQAssistantTypescriptPlugin.sh, detectChangedFiles.sh
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -o errexit -o pipefail
+
+ARTIFACTS_DIRECTORY=${ARTIFACTS_DIRECTORY:-"artifacts"}
+SOURCE_DIRECTORY=${SOURCE_DIRECTORY:-"source"}
+
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+echo "scanTypescript SCRIPTS_DIR=${SCRIPTS_DIR}" >&2
+
+if [ ! -d "./${SOURCE_DIRECTORY}" ] ; then
+    echo "scanTypescript: Source directory '${SOURCE_DIRECTORY}' doesn't exist. The scan will therefore be skipped." >&2
+    return 0
+fi
+
+if ! command -v "npx" &> /dev/null ; then
+    echo "scanTypescript Error: Command npx not found. It's needed to execute @jqassistant/ts-lce to scan Typescript projects." >&2
+    exit 1
+fi
+
+# Scan and analyze Artifacts when they were changed
+changeDetectionHashFilePath="./${SOURCE_DIRECTORY}/typescriptFileChangeDetectionHashFile.txt"
+changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedFiles.sh" --readonly --hashfile "${changeDetectionHashFilePath}" --paths "./${SOURCE_DIRECTORY}")
+
+if [ "${changeDetectionReturnCode}" == "0" ] ; then
+    echo "scanTypescript: Files unchanged. Scan skipped."
+else
+    echo "scanTypescript: Detected change (${changeDetectionReturnCode}). Scanning Typescript source using @jqassistant/ts-lce."
+    
+    # TODO: Remove patchJQAssistantTypescriptPlugin when issue is resolved: https://github.com/jqassistant-plugin/jqassistant-typescript-plugin/issues/125
+    source "${SCRIPTS_DIR}/patchJQAssistantTypescriptPlugin.sh" >&2    
+    
+    # Note: The npx command will be executed in the source directory using a subshell by putting parentheses around it.
+    #       The subshell is the reason why it isn't needed to change back to the main directory after execution.
+    # Note: This script must not output anything except for the return code to stdout,
+    #       all output of the scanning needs to be redirected to stderr using ">&2".
+    #       For later troubleshooting, the output is also copied to a dedicated log file using "tee".
+    # Note: Don't worry about the hardcoded version number. It will be updated by Renovate using a custom Manager.
+    ( cd "./${SOURCE_DIRECTORY}" && npx --yes @jqassistant/ts-lce@1.2.1 --extension React 2>&1 | tee "./../runtime/logs/jqassistant-typescript-scan.log" >&2 || exit )
+    
+    changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedFiles.sh" --hashfile "${changeDetectionHashFilePath}" --paths "./${SOURCE_DIRECTORY}")
+fi
+
+

From efcf4b2614aea01275a09d71d1014d7b21beb145 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 21:33:26 +0200
Subject: [PATCH 14/16] Remove ts-lce patch from commit 291bcec.

Issue jqassistant-plugin/jqassistant-typescript-plugin#125 fixed with @jqassistant/ts-lce@1.2.1.
---
 scripts/patchJQAssistantTypescriptPlugin.sh | 37 ---------------------
 scripts/scanTypescript.sh                   |  3 --
 2 files changed, 40 deletions(-)
 delete mode 100755 scripts/patchJQAssistantTypescriptPlugin.sh

diff --git a/scripts/patchJQAssistantTypescriptPlugin.sh b/scripts/patchJQAssistantTypescriptPlugin.sh
deleted file mode 100755
index eca960c8d..000000000
--- a/scripts/patchJQAssistantTypescriptPlugin.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env bash
-
-# Patches jQAssistant Typescript Plugin as a workaround for https://github.com/jqassistant-plugin/jqassistant-typescript-plugin/issues/125
-
-# Note: As soon as the issue is resolved, this file and its call can be deleted.
-
-# Requires "apply"
-
-# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
-set -o errexit -o pipefail
-
-## Get this "scripts" directory if not already set
-# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
-# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
-# This way non-standard tools like readlink aren't needed.
-SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
-echo "setupJQAssistant: SCRIPTS_DIR=$SCRIPTS_DIR"
-
-if ! command -v "npx" &> /dev/null ; then
-    echo "patchJQAssistantTypescriptPlugin Error: Command npx not found. It's needed to install @jqassistant/ts-lce temporarily."
-fi
-
-echo "patchJQAssistantTypescriptPlugin: Installing jQAssistant Typescript Plugin @jqassistant/ts-lce using npx"
-jqassistant_typescript_plugin_installation_path=$(npx --yes --package @jqassistant/ts-lce@1.2.1 which jqa-ts-lce)
-echo "patchJQAssistantTypescriptPlugin: jqassistant_typescript_plugin_installation_path=${jqassistant_typescript_plugin_installation_path}"
-
-jqassistant_typescript_plugin_bin_path=$(dirname -- "${jqassistant_typescript_plugin_installation_path}")
-jqassistant_typescript_plugin_utils_file_to_patch_relative="${jqassistant_typescript_plugin_bin_path}/../@jqassistant/ts-lce/dist/src/core/utils/project.utils.js"
-echo "patchJQAssistantTypescriptPlugin: jqassistant_typescript_plugin_utils_file_to_patch_relative=${jqassistant_typescript_plugin_utils_file_to_patch_relative}"
-
-jqassistant_typescript_plugin_utils_path_resolved=$( CDPATH=. cd -- "$(dirname -- "${jqassistant_typescript_plugin_utils_file_to_patch_relative}")" && pwd -P )
-jqassistant_typescript_plugin_utils_file_to_patch="${jqassistant_typescript_plugin_utils_path_resolved}/project.utils.js"
-echo "patchJQAssistantTypescriptPlugin: jqassistant_typescript_plugin_utils_file_to_patch=${jqassistant_typescript_plugin_utils_file_to_patch}"
-
-echo "patchJQAssistantTypescriptPlugin: Patching jQAssistant Typescript Plugin @jqassistant/ts-lce"
-patch --forward -p1 "${jqassistant_typescript_plugin_utils_file_to_patch_relative}" -i "${SCRIPTS_DIR}/patches/@jqassistant+ts-lce+1.2.0.patch" || true
-echo "patchJQAssistantTypescriptPlugin: Successfully patched jQAssistant Typescript Plugin @jqassistant/ts-lce"
\ No newline at end of file
diff --git a/scripts/scanTypescript.sh b/scripts/scanTypescript.sh
index 431e278c4..5c2c485d1 100755
--- a/scripts/scanTypescript.sh
+++ b/scripts/scanTypescript.sh
@@ -36,9 +36,6 @@ if [ "${changeDetectionReturnCode}" == "0" ] ; then
 else
     echo "scanTypescript: Detected change (${changeDetectionReturnCode}). Scanning Typescript source using @jqassistant/ts-lce."
     
-    # TODO: Remove patchJQAssistantTypescriptPlugin when issue is resolved: https://github.com/jqassistant-plugin/jqassistant-typescript-plugin/issues/125
-    source "${SCRIPTS_DIR}/patchJQAssistantTypescriptPlugin.sh" >&2    
-    
     # Note: The npx command will be executed in the source directory using a subshell by putting parentheses around it.
     #       The subshell is the reason why it isn't needed to change back to the main directory after execution.
     # Note: This script must not output anything except for the return code to stdout,

From ee279ca150bd0ab61b7920a6f4e32524b1b60562 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 18 Aug 2024 21:57:07 +0200
Subject: [PATCH 15/16] Fix low coupling weight = 0 on when there are no
 declarations

---
 ...script_internal_module_dependencies.cypher | 23 ++++++++++++-------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/cypher/DependsOn_Relationship_Weights/Add_fine_grained_weights_for_Typescript_internal_module_dependencies.cypher b/cypher/DependsOn_Relationship_Weights/Add_fine_grained_weights_for_Typescript_internal_module_dependencies.cypher
index eecea8264..7027141c5 100644
--- a/cypher/DependsOn_Relationship_Weights/Add_fine_grained_weights_for_Typescript_internal_module_dependencies.cypher
+++ b/cypher/DependsOn_Relationship_Weights/Add_fine_grained_weights_for_Typescript_internal_module_dependencies.cypher
@@ -2,14 +2,16 @@
 
 // Get the top level dependency between a Typescript module and the external modules it uses
  MATCH (source:TS:Module)-[moduleDependency:DEPENDS_ON]->(target:Module)
-// Exclude all targets where an ExternalModule was found that resolves to them
-// because those are covered in the fine grained weights for "ExternalModule"s.
- WHERE NOT EXISTS { (target)<-[:RESOLVES_TO]-(resolvedTarget:ExternalModule) }
+// Exclude all that already have extended weight properties
+// for example because those were covered in the fine grained weights for "ExternalModule"s.
+ WHERE moduleDependency.declarationCount IS NULL
+// Ruling out resolved targets also filters out entries that aren't covered by the fine grained weights for "ExternalModule"s.
+// Therefore, the exists filter is commented out for now and replaced by focussing on missing detailed weight properties to catch them all.
+//WHERE NOT EXISTS { (target)<-[:RESOLVES_TO]-(resolvedTarget:ExternalModule) }
   WITH source
       ,target
       ,moduleDependency
       ,moduleDependency.cardinality AS targetModuleCardinality
-
 // Get optional external (e.g. type) declarations that the external module (target) provides and the source module uses
 OPTIONAL MATCH (source)-[elementDependency:DEPENDS_ON|EXPORTS]->(elementType:TS)<-[:EXPORTS]-(target)
   WITH source
@@ -40,13 +42,18 @@ OPTIONAL MATCH (source)-[abstractDependency:DEPENDS_ON|EXPORTS]->(abstractType:T
 // - "lowCouplingElement25PercentWeight" subtracts 75% of the weights for abstract types like Interfaces and Type aliases
 //   to compensate for their low coupling influence. Not included "high coupling" elements like Functions and Classes 
 //   remain in the weight as they were. The same applies for "lowCouplingElement10PercentWeight" but with in a stronger manner.
+//   If there are no declarations and therefore the elementTypeCardinality is zero then the original targetModuleCardinality is used.
  SET moduleDependency.declarationCount        = elementTypeCount
     ,moduleDependency.abstractTypeCount       = abstractTypeCount
     ,moduleDependency.abstractTypeCardinality = abstractTypeCardinality
-    ,moduleDependency.lowCouplingElement25PercentWeight = 
-        toInteger(elementTypeCardinality - round(abstractTypeCardinality * 0.75))
-    ,moduleDependency.lowCouplingElement10PercentWeight = 
-        toInteger(elementTypeCardinality - round(abstractTypeCardinality * 0.90))
+    ,moduleDependency.lowCouplingElement25PercentWeight = toInteger(
+        coalesce(nullif(elementTypeCardinality, 0), targetModuleCardinality) - 
+        round(abstractTypeCardinality * 0.75)
+     )
+    ,moduleDependency.lowCouplingElement10PercentWeight = toInteger(
+        coalesce(nullif(elementTypeCardinality, 0), targetModuleCardinality) - 
+        round(abstractTypeCardinality * 0.90)
+     )
 RETURN source.globalFqn    AS sourceName
       ,target.globalFqn    AS targetName
       ,elementTypeCount

From 29addeb673cb7ce411dbe0f76d85bbd54d112f83 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Mon, 19 Aug 2024 15:34:56 +0200
Subject: [PATCH 16/16] Fix missing runtime logs directory on Windows

---
 scripts/scanTypescript.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/scanTypescript.sh b/scripts/scanTypescript.sh
index 5c2c485d1..fd87171cf 100755
--- a/scripts/scanTypescript.sh
+++ b/scripts/scanTypescript.sh
@@ -42,6 +42,7 @@ else
     #       all output of the scanning needs to be redirected to stderr using ">&2".
     #       For later troubleshooting, the output is also copied to a dedicated log file using "tee".
     # Note: Don't worry about the hardcoded version number. It will be updated by Renovate using a custom Manager.
+    mkdir -p "./runtime/logs"
     ( cd "./${SOURCE_DIRECTORY}" && npx --yes @jqassistant/ts-lce@1.2.1 --extension React 2>&1 | tee "./../runtime/logs/jqassistant-typescript-scan.log" >&2 || exit )
     
     changeDetectionReturnCode=$( source "${SCRIPTS_DIR}/detectChangedFiles.sh" --hashfile "${changeDetectionHashFilePath}" --paths "./${SOURCE_DIRECTORY}")