CodeQL codesign error message

github/codeql-action/init@v2 のワークフローステップから始め、初期化ありと初期化なしで Fastlane のビルド出力を比較します。調査の手がかりとして CodeSign の失敗とデバッグログのエントリを使用します。署名が置き換えられる理由と、その置き換えが失敗するスキャンの原因になっているかどうかを説明できれば完了です。

We`re workin on CodeQL Static Application Security Testing (SAST) implementation for a Swift language using GitHub Actions. During this process, I encountered an issue with the CodeQL initialization step when integrating with a Fastlane-based build process.

When including the CodeQL initialization step (github/codeql-action/init@v2) in the GitHub Actions workflow before Fastlane-based build commands, the build job fails with a CodeSign error. The specific error message indicates that the CodeSign command has failed.

Interesting Behavior: if I remove the CodeQL initialization step from the GitHub Actions workflow, the build application process works perfectly without any issues - application builds well.

Error message from console output:

▸ ** ARCHIVE FAILED **
▸ The following build commands failed:
▸ 	CodeSign /Users/runner/Library/Developer/Xcode/DerivedData/APP-amdyapuwajsvoeelnrjmqpntrblu/Build/Intermediates.noindex/ArchiveIntermediates/APP_straging/IntermediateBuildFilesPath/UninstalledProducts/iphoneos/SaleforceNotificationService_staging.appex (in target 'SaleforceNotificationService_staging' from project 'APP')
▸ (1 failure)

From debug logs we got below entries:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: warning: changes being made to the file will invalidate the code signature in: /Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang-stat-cache.semmle.00008433.slice.x86_64
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang-stat-cache.semmle.00008433.slice.x86_64: replacing existing signature
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: warning: changes being made to the file will invalidate the code signature in: /Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang-stat-cache.semmle.00008433.slice.arm64
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang-stat-cache.semmle.00008433.slice.arm64: replacing existing signature
[T 17:01:12 33906] Attempting to switch stdout/stderr to 7...
[T 17:01:12 33908] Attempting to switch stdout/stderr to 7...
[T 17:01:12 33909] Attempting to switch stdout/stderr to 7...
[T 17:01:12 33913] Attempting to switch stdout/stderr to 7...
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/usr/bin/codesign.semmle.00008433.145DE1E8.slice.x86_64: replacing existing signature
[T 17:01:12 33914] Attempting to switch stdout/stderr to 7...
[T 17:01:12 33912] Initializing tracer.
[T 17:01:12 33912] Initialising tags...
[T 17:01:12 33912] ID set to 0000000000008478_0000000000000001 (parent 0000000000008433_0000000000000001)
[T 17:01:12 33912] ==== Candidate to intercept: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang-stat-cache (canonical: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang-stat-cache) ====
[T 17:01:12 33912] Executing the following tracer actions:
[T 17:01:12 33912] Tracer actions:
[T 17:01:12 33912] pre_invocations(0)
[T 17:01:12 33912] post_invocations(0)
[T 17:01:12 33912] trace_languages(1): [swift]
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/usr/bin/codesign.semmle.00008433.slice.x86_64: replacing existing signature
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/usr/bin/codesign.semmle.00008433.slice.x86_64: replacing existing signature
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/usr/bin/codesign.semmle.00008433.slice.x86_64: replacing existing signature
/Users/runner/actions-runner/_work/_temp/codeql_databases/working/copy-root/000001F6/usr/bin/codesign.semmle.00008433.slice.x86_64: replacing existing signature

Why codeql replace signature and is it the case for failing our scan ?