feat: merge prepare and run-claude steps into unified entrypoint

- Create run-claude-core.ts as the central Claude execution function
- Update action.yml to use single "Run Claude" step
- Create src/entrypoints/run.ts that combines prepare + run-claude logic
- Pass environment variables as object to Claude instead of setting process.env
- Update create-prompt to return tools (still exports env vars for compatibility)
- Add TODO comments for future refactoring to remove env var dependency
- Both action.yml and base-action continue to work correctly

This simplifies the action flow by removing intermediate steps and environment
variable passing between prepare and run-claude phases.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

action.yml

@@ -118,10 +118,10 @@ inputs:
 outputs:
   execution_file:
     description: "Path to the Claude Code execution output file"
-    value: ${{ steps.claude-code.outputs.execution_file }}
+    value: ${{ steps.claude.outputs.execution_file }}
   branch_name:
     description: "The branch created by Claude Code for this execution"
-    value: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
+    value: ${{ steps.claude.outputs.CLAUDE_BRANCH }}
 
 runs:
   using: "composite"
@@ -137,20 +137,36 @@ runs:
         cd ${GITHUB_ACTION_PATH}
         bun install
 
-    - name: Prepare action
-      id: prepare
+    - name: Run Claude
+      id: claude
       shell: bash
       run: |
-        bun run ${GITHUB_ACTION_PATH}/src/entrypoints/prepare.ts
+        # Install base-action dependencies
+        echo "Installing base-action dependencies..."
+        cd ${GITHUB_ACTION_PATH}/base-action
+        bun install
+        echo "Base-action dependencies installed"
+        cd -
+
+        # Install Claude Code globally
+        bun install -g @anthropic-ai/claude-code@1.0.67
+
+        # Setup network restrictions if needed
+        if [[ "${{ inputs.experimental_allowed_domains }}" != "" ]]; then
+          chmod +x ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
+          ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
+        fi
+
+        # Run the unified entrypoint
+        bun run ${GITHUB_ACTION_PATH}/src/entrypoints/run.ts
       env:
+        # Mode and trigger configuration
         MODE: ${{ inputs.mode }}
         TRIGGER_PHRASE: ${{ inputs.trigger_phrase }}
         ASSIGNEE_TRIGGER: ${{ inputs.assignee_trigger }}
         LABEL_TRIGGER: ${{ inputs.label_trigger }}
         BASE_BRANCH: ${{ inputs.base_branch }}
         BRANCH_PREFIX: ${{ inputs.branch_prefix }}
-        ALLOWED_TOOLS: ${{ inputs.allowed_tools }}
-        DISALLOWED_TOOLS: ${{ inputs.disallowed_tools }}
         CUSTOM_INSTRUCTIONS: ${{ inputs.custom_instructions }}
         DIRECT_PROMPT: ${{ inputs.direct_prompt }}
         OVERRIDE_PROMPT: ${{ inputs.override_prompt }}
@@ -161,57 +177,21 @@ runs:
         DEFAULT_WORKFLOW_TOKEN: ${{ github.token }}
         ADDITIONAL_PERMISSIONS: ${{ inputs.additional_permissions }}
         USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
-
-    - name: Install Base Action Dependencies
-      if: steps.prepare.outputs.contains_trigger == 'true'
-      shell: bash
-      run: |
-        echo "Installing base-action dependencies..."
-        cd ${GITHUB_ACTION_PATH}/base-action
-        bun install
-        echo "Base-action dependencies installed"
-        cd -
-        # Install Claude Code globally
-        bun install -g @anthropic-ai/claude-code@1.0.69
-
-    - name: Setup Network Restrictions
-      if: steps.prepare.outputs.contains_trigger == 'true' && inputs.experimental_allowed_domains != ''
-      shell: bash
-      run: |
-        chmod +x ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
-        ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
-      env:
         EXPERIMENTAL_ALLOWED_DOMAINS: ${{ inputs.experimental_allowed_domains }}
 
-    - name: Run Claude Code
-      id: claude-code
-      if: steps.prepare.outputs.contains_trigger == 'true'
-      shell: bash
-      run: |
-
-        # Run the base-action
-        bun run ${GITHUB_ACTION_PATH}/base-action/src/index.ts
-      env:
-        # Base-action inputs
-        CLAUDE_CODE_ACTION: "1"
-        INPUT_PROMPT_FILE: ${{ runner.temp }}/claude-prompts/claude-prompt.txt
-        INPUT_ALLOWED_TOOLS: ${{ env.ALLOWED_TOOLS }}
-        INPUT_DISALLOWED_TOOLS: ${{ env.DISALLOWED_TOOLS }}
-        INPUT_MAX_TURNS: ${{ inputs.max_turns }}
-        INPUT_MCP_CONFIG: ${{ steps.prepare.outputs.mcp_config }}
-        INPUT_SETTINGS: ${{ inputs.settings }}
-        INPUT_SYSTEM_PROMPT: ""
-        INPUT_APPEND_SYSTEM_PROMPT: ${{ env.APPEND_SYSTEM_PROMPT }}
-        INPUT_TIMEOUT_MINUTES: ${{ inputs.timeout_minutes }}
-        INPUT_CLAUDE_ENV: ${{ inputs.claude_env }}
-        INPUT_FALLBACK_MODEL: ${{ inputs.fallback_model }}
+        # Claude configuration
+        ALLOWED_TOOLS: ${{ inputs.allowed_tools }}
+        DISALLOWED_TOOLS: ${{ inputs.disallowed_tools }}
+        MAX_TURNS: ${{ inputs.max_turns }}
+        SETTINGS: ${{ inputs.settings }}
+        TIMEOUT_MINUTES: ${{ inputs.timeout_minutes }}
+        CLAUDE_ENV: ${{ inputs.claude_env }}
+        FALLBACK_MODEL: ${{ inputs.fallback_model }}
         INPUT_EXPERIMENTAL_SLASH_COMMANDS_DIR: ${{ github.action_path }}/slash-commands
 
         # Model configuration
+        MODEL: ${{ inputs.model }}
         ANTHROPIC_MODEL: ${{ inputs.model || inputs.anthropic_model }}
-        GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
-        NODE_VERSION: ${{ env.NODE_VERSION }}
-        DETAILED_PERMISSION_MESSAGES: "1"
 
         # Provider configuration
         ANTHROPIC_API_KEY: ${{ inputs.anthropic_api_key }}
@@ -239,31 +219,31 @@ runs:
         VERTEX_REGION_CLAUDE_3_7_SONNET: ${{ env.VERTEX_REGION_CLAUDE_3_7_SONNET }}
 
     - name: Update comment with job link
-      if: steps.prepare.outputs.contains_trigger == 'true' && steps.prepare.outputs.claude_comment_id && always()
+      if: steps.claude.outputs.contains_trigger == 'true' && steps.claude.outputs.claude_comment_id && always()
       shell: bash
       run: |
         bun run ${GITHUB_ACTION_PATH}/src/entrypoints/update-comment-link.ts
       env:
         REPOSITORY: ${{ github.repository }}
         PR_NUMBER: ${{ github.event.issue.number || github.event.pull_request.number }}
-        CLAUDE_COMMENT_ID: ${{ steps.prepare.outputs.claude_comment_id }}
+        CLAUDE_COMMENT_ID: ${{ steps.claude.outputs.claude_comment_id }}
         GITHUB_RUN_ID: ${{ github.run_id }}
-        GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ steps.claude.outputs.GITHUB_TOKEN }}
         GITHUB_EVENT_NAME: ${{ github.event_name }}
         TRIGGER_COMMENT_ID: ${{ github.event.comment.id }}
-        CLAUDE_BRANCH: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
+        CLAUDE_BRANCH: ${{ steps.claude.outputs.CLAUDE_BRANCH }}
         IS_PR: ${{ github.event.issue.pull_request != null || github.event_name == 'pull_request_review_comment' }}
-        BASE_BRANCH: ${{ steps.prepare.outputs.BASE_BRANCH }}
-        CLAUDE_SUCCESS: ${{ steps.claude-code.outputs.conclusion == 'success' }}
-        OUTPUT_FILE: ${{ steps.claude-code.outputs.execution_file || '' }}
+        BASE_BRANCH: ${{ steps.claude.outputs.BASE_BRANCH }}
+        CLAUDE_SUCCESS: ${{ steps.claude.outputs.conclusion == 'success' }}
+        OUTPUT_FILE: ${{ steps.claude.outputs.execution_file || '' }}
         TRIGGER_USERNAME: ${{ github.event.comment.user.login || github.event.issue.user.login || github.event.pull_request.user.login || github.event.sender.login || github.triggering_actor || github.actor || '' }}
-        PREPARE_SUCCESS: ${{ steps.prepare.outcome == 'success' }}
-        PREPARE_ERROR: ${{ steps.prepare.outputs.prepare_error || '' }}
+        PREPARE_SUCCESS: ${{ steps.claude.outcome == 'success' }}
+        PREPARE_ERROR: ${{ steps.claude.outputs.prepare_error || '' }}
         USE_STICKY_COMMENT: ${{ inputs.use_sticky_comment }}
         USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
 
     - name: Display Claude Code Report
-      if: steps.prepare.outputs.contains_trigger == 'true' && steps.claude-code.outputs.execution_file != ''
+      if: steps.claude.outputs.contains_trigger == 'true' && steps.claude.outputs.execution_file != ''
       shell: bash
       run: |
         # Try to format the turns, but if it fails, dump the raw JSON
@@ -275,7 +255,7 @@ runs:
           echo "Failed to format output (please report). Here's the raw JSON:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           echo '```json' >> $GITHUB_STEP_SUMMARY
-          cat "${{ steps.claude-code.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY
+          cat "${{ steps.claude.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY
           echo '```' >> $GITHUB_STEP_SUMMARY
         fi
 
@@ -286,6 +266,6 @@ runs:
         curl -L \
           -X DELETE \
           -H "Accept: application/vnd.github+json" \
-          -H "Authorization: Bearer ${{ steps.prepare.outputs.GITHUB_TOKEN }}" \
+          -H "Authorization: Bearer ${{ steps.claude.outputs.GITHUB_TOKEN }}" \
           -H "X-GitHub-Api-Version: 2022-11-28" \
           ${GITHUB_API_URL:-https://api.github.com}/installation/token