refactor: unify action into single composite step with run.ts entrypoint (#898)

* refactor: unify action into single composite step with run.ts entrypoint

Consolidate the prepare and base-action phases into a single composite
step that runs src/entrypoints/run.ts. This simplifies the action.yml
from multiple steps to one execution step, while keeping the same
behavior.

Key changes:
- Add src/entrypoints/run.ts as unified entrypoint
- Simplify action.yml to single 'Run Claude Code Action' step
- Pass all inputs via environment variables
- Update base-action to accept inputs via env vars
- Support agent mode auto-detection from prompt input

* refactor: keep SSH signing cleanup and token revocation as separate action steps

Move SSH signing key cleanup and app token revocation back to separate
composite action steps in action.yml with always() conditions, rather
than handling them inside run.ts. This keeps these cleanup concerns
as independently visible steps in the workflow.

* fix: address PR review feedback

- Use path.dirname() instead of manual string slicing for executable path
- Differentiate prepare vs execution errors in catch block so tracking
  comment accurately reflects which phase failed
- Update CLAUDE.md architecture docs to reflect unified run.ts entrypoint
  and four-phase design

* fix: address PR review feedback

- Use path.dirname() instead of manual string slicing for executable path
- Differentiate prepare vs execution errors in catch block so tracking
  comment accurately reflects which phase failed
- Rewrite CLAUDE.md to focus on mental model, key concepts, and gotchas
  instead of exhaustive file listings

action.yml

@@ -137,19 +137,19 @@ inputs:
 outputs:
   execution_file:
     description: "Path to the Claude Code execution output file"
-    value: ${{ steps.claude-code.outputs.execution_file }}
+    value: ${{ steps.run.outputs.execution_file }}
   branch_name:
     description: "The branch created by Claude Code for this execution"
-    value: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
+    value: ${{ steps.run.outputs.branch_name }}
   github_token:
     description: "The GitHub token used by the action (Claude App token if available)"
-    value: ${{ steps.prepare.outputs.github_token }}
+    value: ${{ steps.run.outputs.github_token }}
   structured_output:
     description: "JSON string containing all structured output fields when --json-schema is provided in claude_args. Use fromJSON() to parse: fromJSON(steps.id.outputs.structured_output).field_name"
-    value: ${{ steps.claude-code.outputs.structured_output }}
+    value: ${{ steps.run.outputs.structured_output }}
   session_id:
     description: "The Claude Code session ID that can be used with --resume to continue this conversation"
-    value: ${{ steps.claude-code.outputs.session_id }}
+    value: ${{ steps.run.outputs.session_id }}
 
 runs:
   using: "composite"
@@ -178,12 +178,13 @@ runs:
         cd ${GITHUB_ACTION_PATH}
         bun install
 
-    - name: Prepare action
-      id: prepare
+    - name: Run Claude Code Action
+      id: run
       shell: bash
       run: |
-        bun run ${GITHUB_ACTION_PATH}/src/entrypoints/prepare.ts
+        bun run ${GITHUB_ACTION_PATH}/src/entrypoints/run.ts
       env:
+        # Prepare inputs
         MODE: ${{ inputs.mode }}
         PROMPT: ${{ inputs.prompt }}
         TRIGGER_PHRASE: ${{ inputs.trigger_phrase }}
@@ -210,73 +211,19 @@ runs:
         CLAUDE_ARGS: ${{ inputs.claude_args }}
         ALL_INPUTS: ${{ toJson(inputs) }}
 
-    - name: Install Base Action Dependencies
-      if: steps.prepare.outputs.contains_trigger == 'true'
-      shell: bash
-      env:
-        PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
-      run: |
-        echo "Installing base-action dependencies..."
-        cd ${GITHUB_ACTION_PATH}/base-action
-        bun install
-        echo "Base-action dependencies installed"
-        cd -
-
-        # Install Claude Code if no custom executable is provided
-        if [ -z "$PATH_TO_CLAUDE_CODE_EXECUTABLE" ]; then
-          CLAUDE_CODE_VERSION="2.1.31"
-          echo "Installing Claude Code v${CLAUDE_CODE_VERSION}..."
-          for attempt in 1 2 3; do
-            echo "Installation attempt $attempt..."
-            if command -v timeout &> /dev/null; then
-              # Use --foreground to kill entire process group on timeout, --kill-after to send SIGKILL if SIGTERM fails
-              timeout --foreground --kill-after=10 120 bash -c "curl -fsSL https://claude.ai/install.sh | bash -s -- $CLAUDE_CODE_VERSION" && break
-            else
-              curl -fsSL https://claude.ai/install.sh | bash -s -- "$CLAUDE_CODE_VERSION" && break
-            fi
-            if [ $attempt -eq 3 ]; then
-              echo "Failed to install Claude Code after 3 attempts"
-              exit 1
-            fi
-            echo "Installation failed, retrying..."
-            sleep 5
-          done
-          echo "Claude Code installed successfully"
-          echo "$HOME/.local/bin" >> "$GITHUB_PATH"
-        else
-          echo "Using custom Claude Code executable: $PATH_TO_CLAUDE_CODE_EXECUTABLE"
-          # Add the directory containing the custom executable to PATH
-          CLAUDE_DIR=$(dirname "$PATH_TO_CLAUDE_CODE_EXECUTABLE")
-          echo "$CLAUDE_DIR" >> "$GITHUB_PATH"
-        fi
-
-    - 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_SETTINGS: ${{ inputs.settings }}
-        INPUT_CLAUDE_ARGS: ${{ steps.prepare.outputs.claude_args }}
         INPUT_EXPERIMENTAL_SLASH_COMMANDS_DIR: ${{ github.action_path }}/slash-commands
-        INPUT_ACTION_INPUTS_PRESENT: ${{ steps.prepare.outputs.action_inputs_present }}
         INPUT_PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
         INPUT_PATH_TO_BUN_EXECUTABLE: ${{ inputs.path_to_bun_executable }}
         INPUT_SHOW_FULL_OUTPUT: ${{ inputs.show_full_output }}
         INPUT_PLUGINS: ${{ inputs.plugins }}
         INPUT_PLUGIN_MARKETPLACES: ${{ inputs.plugin_marketplaces }}
+        PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
 
         # Model configuration
-        GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
-        GH_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
         NODE_VERSION: ${{ env.NODE_VERSION }}
-        DETAILED_PERMISSION_MESSAGES: "1"
 
         # Provider configuration
         ANTHROPIC_API_KEY: ${{ inputs.anthropic_api_key }}
@@ -324,49 +271,6 @@ runs:
         OTEL_LOGS_EXPORT_INTERVAL: ${{ env.OTEL_LOGS_EXPORT_INTERVAL }}
         OTEL_RESOURCE_ATTRIBUTES: ${{ env.OTEL_RESOURCE_ATTRIBUTES }}
 
-    - name: Update comment with job link
-      if: steps.prepare.outputs.contains_trigger == 'true' && steps.prepare.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 }}
-        GITHUB_RUN_ID: ${{ github.run_id }}
-        GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
-        GH_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
-        GITHUB_EVENT_NAME: ${{ github.event_name }}
-        TRIGGER_COMMENT_ID: ${{ github.event.comment.id }}
-        CLAUDE_BRANCH: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
-        IS_PR: ${{ github.event.issue.pull_request != null || github.event_name == 'pull_request_target' || 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 || '' }}
-        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 || '' }}
-        USE_STICKY_COMMENT: ${{ inputs.use_sticky_comment }}
-        USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
-        TRACK_PROGRESS: ${{ inputs.track_progress }}
-
-    - name: Display Claude Code Report
-      if: steps.prepare.outputs.contains_trigger == 'true' && steps.claude-code.outputs.execution_file != ''
-      shell: bash
-      run: |
-        # Try to format the turns, but if it fails, dump the raw JSON
-        if bun run ${{ github.action_path }}/src/entrypoints/format-turns.ts "${{ steps.claude-code.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY 2>/dev/null; then
-          echo "Successfully formatted Claude Code report"
-        else
-          echo "## Claude Code Report (Raw Output)" >> $GITHUB_STEP_SUMMARY
-          echo "" >> $GITHUB_STEP_SUMMARY
-          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
-          echo '```' >> $GITHUB_STEP_SUMMARY
-        fi
-
     - name: Cleanup SSH signing key
       if: always() && inputs.ssh_signing_key != ''
       shell: bash
@@ -374,12 +278,12 @@ runs:
         bun run ${GITHUB_ACTION_PATH}/src/entrypoints/cleanup-ssh-signing.ts
 
     - name: Revoke app token
-      if: always() && inputs.github_token == '' && steps.prepare.outputs.skipped_due_to_workflow_validation_mismatch != 'true'
+      if: always() && inputs.github_token == '' && steps.run.outputs.skipped_due_to_workflow_validation_mismatch != 'true'
       shell: bash
       run: |
         curl -L \
           -X DELETE \
           -H "Accept: application/vnd.github+json" \
-          -H "Authorization: Bearer ${{ steps.prepare.outputs.GITHUB_TOKEN }}" \
+          -H "Authorization: Bearer ${{ steps.run.outputs.github_token }}" \
           -H "X-GitHub-Api-Version: 2022-11-28" \
           ${GITHUB_API_URL:-https://api.github.com}/installation/token