Merge changes

Author: KevinMwita7

.github/CODEOWNERS

@@ -1 +1 @@
-* @DenizAltunkapan @yanglbme @vil02 @BamaCharanChhandogi @alxkm @siriak
+* @DenizAltunkapan @yanglbme @vil02 @alxkm

.github/workflows/build.yml

@@ -1,6 +1,9 @@
 name: Build
 on: [push, pull_request]
 
+permissions:
+  contents: read
+
 jobs:
   build:
     runs-on: ubuntu-latest

.github/workflows/clang-format-lint.yml

@@ -3,6 +3,9 @@ on:
   push: {}
   pull_request: {}
 
+permissions:
+  contents: read
+
 jobs:
   build:
     runs-on: ubuntu-latest

.github/workflows/codeql.yml

@@ -10,12 +10,9 @@ on:
   schedule:
     - cron: '53 3 * * 0'
 
-env:
-  LANGUAGE: 'java-kotlin'
-
 jobs:
-  analyze:
-    name: Analyze
+  analyzeJava:
+    name: AnalyzeJava
     runs-on: 'ubuntu-latest'
     permissions:
       actions: read
@@ -35,13 +32,35 @@ jobs:
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3
         with:
-          languages: ${{ env.LANGUAGE }}
+          languages: 'java-kotlin'
 
       - name: Build
         run: mvn --batch-mode --update-snapshots verify
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v3
         with:
-          category: "/language:${{env.LANGUAGE}}"
+          category: "/language:java-kotlin"
+
+  analyzeActions:
+    name: AnalyzeActions
+    runs-on: 'ubuntu-latest'
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: 'actions'
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:actions"
 ...

.github/workflows/infer.yml

@@ -8,6 +8,9 @@ name: Infer
       - master
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   run_infer:
     runs-on: ubuntu-latest

.github/workflows/project_structure.yml

@@ -8,6 +8,9 @@ name: ProjectStructure
       - master
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   check_structure:
     runs-on: ubuntu-latest

.github/workflows/stale.yml

@@ -2,8 +2,13 @@ name: 'Close stale issues and PRs'
 on:
   schedule:
     - cron: '0 0 * * *'
+permissions:
+  contents: read
 jobs:
   stale:
+    permissions:
+      issues: write
+      pull-requests: write
     runs-on: ubuntu-latest
     steps:
       - uses: actions/stale@v9

.github/workflows/update-directorymd.yml

@@ -0,0 +1,42 @@
+name: Generate Directory Markdown
+
+on:
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  generate-directory:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Run Directory Tree Generator
+        uses: DenizAltunkapan/directory-tree-generator@v2
+        with:
+          path: src
+          extensions: .java
+          show-extensions: false
+
+      - name: Commit changes
+        run: |
+          git config --global user.name "$GITHUB_ACTOR"
+          git config --global user.email "[email protected]"
+          git add DIRECTORY.md
+          git diff --cached --quiet || git commit -m "Update DIRECTORY.md"
+      
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.REPO_SCOPED_TOKEN }}
+          branch: update-directory
+          base: master
+          title: "Update DIRECTORY.md"
+          body: "Automatically generated update of the directory tree."
+          commit-message: "Update DIRECTORY.md"
+          draft: false

.github/workflows/update_directory.yml

@@ -1,4 +1,4 @@
-FROM gitpod/workspace-java-21:2025-05-14-07-50-25
+FROM gitpod/workspace-java-21:2025-06-18-16-47-14
 
 ENV LLVM_SCRIPT="tmp_llvm.sh"