diff --git a/.gitignore b/.gitignore
index eba74f4..53ac36d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,3 @@
-venv/
\ No newline at end of file
+venv/
+__pycache__/
+*.pyc
\ No newline at end of file
diff --git a/README.md b/README.md
index 62d1045..df9bcb6 100644
--- a/README.md
+++ b/README.md
@@ -29,8 +29,18 @@ on:
 jobs:
   create-matrix:
     runs-on: ubuntu-latest
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
     outputs:
-      matrix: ${{ steps.set-matrix.outputs.languages }}
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: Get languages from repo
         id: set-matrix
@@ -43,7 +53,7 @@ jobs:
     needs: create-matrix
     if: ${{ needs.create-matrix.outputs.matrix != '[]' }}
     name: Analyze
-    runs-on: ubuntu-latest
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
     permissions:
       actions: read
       contents: read
@@ -51,8 +61,7 @@ jobs:
 
     strategy:
       fail-fast: false
-      matrix: 
-        language: ${{ fromJSON(needs.create-matrix.outputs.matrix) }}
+      matrix: ${{ fromJSON(needs.create-matrix.outputs.matrix) }}
 
     steps:
     - name: Checkout repository
@@ -63,10 +72,17 @@ jobs:
       uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
- 
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
+        build-mode: ${{ matrix.build-mode }}
+
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@v3
@@ -82,7 +98,7 @@ Example:
   create-matrix:
     runs-on: ubuntu-latest
     outputs:
-      matrix: ${{ steps.set-matrix.outputs.languages }}
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: Get languages from repo
         id: set-matrix
@@ -94,6 +110,28 @@ Example:
 
 ```
 
+### Build Mode Override
+By default, the action sets the build mode to:
+- `none` for most languages (python, javascript, ruby, rust, actions, etc.)
+- `manual` for languages that typically require custom build steps (go, swift, java)
+
+If you want to override this behavior and use manual build mode for specific languages, use the `build-mode-manual-override` input:
+
+``` yaml
+  create-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: Get languages from repo
+        id: set-matrix
+        uses: advanced-security/set-codeql-language-matrix@v1
+        with:
+          access-token: ${{ secrets.GITHUB_TOKEN }}
+          endpoint: ${{ github.event.repository.languages_url }}
+          build-mode-manual-override: 'java, csharp'
+```
+
 ### Actions support
 
 The GitHub API for [List repository languages](https://docs.github.com/en/rest/repos/repos?apiVersion=2022-11-28#list-repository-languages) does not by default include "YAML"/"GitHub Actions". This is particularly useful if your repository contains GitHub Actions workflows that you want to include in CodeQL analysis.
diff --git a/action.yml b/action.yml
index cdca95e..f54207f 100644
--- a/action.yml
+++ b/action.yml
@@ -12,9 +12,14 @@ inputs:
   exclude:
     description: 'Use a comma separated list here to exclude specific languges from your CodeQL scan.  Example: "python, java"'
     required: false
+  build-mode-manual-override:
+    description: 'Use a comma separated list here to specify languages that should use manual build mode instead of the default. Example: "java, csharp"'
+    required: false
 outputs:
+  matrix:
+    description: 'Matrix definition including language and build-mode configurations'
   languages:
-    description: 'List of languages that will set the job matrix'
+    description: 'List of languages that will set the job matrix (deprecated - use matrix instead)'
 runs:
   using: 'docker'
   image: 'Dockerfile'
@@ -22,4 +27,5 @@ runs:
    - ${{ inputs.access-token }}
    - ${{ inputs.endpoint }}
    - ${{ inputs.exclude }}
+   - ${{ inputs.build-mode-manual-override }}
 
diff --git a/entrypoint.sh b/entrypoint.sh
index 2424ea5..2280414 100755
--- a/entrypoint.sh
+++ b/entrypoint.sh
@@ -1,4 +1,4 @@
 #!/bin/sh -l
 
 # kick off the command
-python /main.py $1 $2 "$3"
\ No newline at end of file
+python /main.py $1 $2 "$3" "$4"
\ No newline at end of file
diff --git a/main.py b/main.py
index 7480e4e..afd4a2f 100644
--- a/main.py
+++ b/main.py
@@ -5,7 +5,8 @@
 
 token = sys.argv[1]
 endpoint = sys.argv[2]
-exclude = sys.argv[3]
+exclude = sys.argv[3] if len(sys.argv) > 3 else ""
+build_mode_manual_override = sys.argv[4] if len(sys.argv) > 4 else ""
 codeql_languages = ["actions", "cpp", "csharp", "go", "java", "javascript", "python", "ruby", "rust", "typescript", "kotlin", "swift"]
 
 
@@ -17,32 +18,93 @@ def get_languages():
 
 # Find the intersection of the languages returned by the API and the languages supported by CodeQL
 def build_languages_list(languages):
-    languages = [language.lower() for language in languages.keys()]
-    for i in range(len(languages)):
-        if languages[i] == "c#":
-            languages[i] = ("csharp")
-        if languages[i] == "c++":
-            languages[i] = ("cpp")
-        if languages[i] == "c":
-            languages[i] = ("cpp")
-        if languages[i] == "typescript":
-            languages[i] = ("javascript")
-        if languages[i] == "kotlin":
-            languages[i] = ("java")
-        if languages[i] == "yaml":
-            languages[i] = ("actions")
-    print("After mapping:", languages)
-    intersection = list(set(languages) & set(codeql_languages))
+    original_languages = [language.lower() for language in languages.keys()]
+    mapped_languages = []
+    language_mapping = {}  # Track mapped language -> list of original languages
+    
+    for orig_lang in original_languages:
+        mapped_lang = orig_lang
+        if orig_lang == "c#":
+            mapped_lang = "csharp"
+        elif orig_lang == "c++":
+            mapped_lang = "cpp"
+        elif orig_lang == "c":
+            mapped_lang = "cpp"
+        elif orig_lang == "typescript":
+            mapped_lang = "javascript"
+        elif orig_lang == "kotlin":
+            mapped_lang = "java"
+        elif orig_lang == "yaml":
+            mapped_lang = "actions"
+        
+        mapped_languages.append(mapped_lang)
+        
+        # Track all original languages that map to this CodeQL language
+        if mapped_lang not in language_mapping:
+            language_mapping[mapped_lang] = []
+        language_mapping[mapped_lang].append(orig_lang)
+    
+    print("After mapping:", mapped_languages)
+    intersection = list(set(mapped_languages) & set(codeql_languages))
     print("Intersection:", intersection)
-    return intersection
+    return intersection, language_mapping
 
 # return a list of objects from language list if they are not in the exclude list
 def exclude_languages(language_list):
+    if not exclude:
+        return language_list
     excluded = [x.strip() for x in exclude.split(',')]
     output = list(set(language_list).difference(excluded))
     print("languages={}".format(output))
     return output
 
+# Determine build mode for each language
+def get_build_mode(language, original_languages=None):
+    # Languages that should use manual build mode by default
+    # Check original languages first if available
+    if original_languages:
+        # If any of the original languages require manual build mode, use manual
+        for orig_lang in original_languages:
+            if orig_lang in ["kotlin", "go", "swift"]:
+                manual_by_default = True
+                break
+        else:
+            manual_by_default = False
+    else:
+        # Fallback to mapped language check
+        manual_by_default = language in ["go", "swift", "java"]
+    
+    # Check if user overrode build mode to manual
+    if build_mode_manual_override:
+        override_languages = [x.strip() for x in build_mode_manual_override.split(',')]
+        if language in override_languages:
+            return "manual"
+        if original_languages:
+            for orig_lang in original_languages:
+                if orig_lang in override_languages:
+                    return "manual"
+    
+    # Use default logic
+    if manual_by_default:
+        return "manual"
+    else:
+        return "none"
+
+# Build the matrix include format
+def build_matrix(language_list, language_mapping):
+    include = []
+    for language in language_list:
+        original_languages = language_mapping.get(language, [language])
+        build_mode = get_build_mode(language, original_languages)
+        include.append({
+            "language": language,
+            "build-mode": build_mode
+        })
+    
+    matrix = {"include": include}
+    print("Matrix:", matrix)
+    return matrix
+
 # Set the output of the action
 def set_action_output(output_name, value) :
     if "GITHUB_OUTPUT" in os.environ :
@@ -51,9 +113,12 @@ def set_action_output(output_name, value) :
 
 def main():
     languages = get_languages()
-    language_list = build_languages_list(languages)
-    output = exclude_languages(language_list)
-    set_action_output("languages", json.dumps(output))
+    language_list, language_mapping = build_languages_list(languages)
+    filtered_languages = exclude_languages(language_list)
+    matrix = build_matrix(filtered_languages, language_mapping)
+    set_action_output("matrix", json.dumps(matrix))
+    # Keep the old output for backward compatibility
+    set_action_output("languages", json.dumps(filtered_languages))
 
 if __name__ == '__main__':
     main()