Update usage.md with link to claude cli args (#600)

Clarifies which permissions are currently used (Contents, Pull Requests, Issues) versus those requested for planned future features (Discussions, Actions, Checks, Workflows).

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

Co-authored-by: Claude <noreply@anthropic.com>

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - uses: oven-sh/setup-bun@v2
         with:
@@ -24,7 +24,7 @@ jobs:
   prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - uses: oven-sh/setup-bun@v1
         with:
@@ -39,7 +39,7 @@ jobs:
   typecheck:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - uses: oven-sh/setup-bun@v2
         with:

.github/workflows/claude-review.yml

@@ -13,7 +13,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

.github/workflows/claude.yml

@@ -25,7 +25,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

.github/workflows/issue-triage.yml

@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
       next_version: ${{ steps.next_version.outputs.next_version }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -91,7 +91,7 @@ jobs:
       contents: write
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -116,7 +116,7 @@ jobs:
     environment: production
     steps:
       - name: Checkout base-action repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           repository: anthropics/claude-code-base-action
           token: ${{ secrets.CLAUDE_CODE_BASE_ACTION_PAT }}

action.yml

@@ -177,7 +177,7 @@ runs:
         # Install Claude Code if no custom executable is provided
         if [ -z "${{ inputs.path_to_claude_code_executable }}" ]; then
           echo "Installing Claude Code..."
-          curl -fsSL https://claude.ai/install.sh | bash -s 2.0.13
+          curl -fsSL https://claude.ai/install.sh | bash -s 2.0.25
           echo "$HOME/.local/bin" >> "$GITHUB_PATH"
         else
           echo "Using custom Claude Code executable: ${{ inputs.path_to_claude_code_executable }}"

base-action/README.md

@@ -336,7 +336,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 

base-action/action.yml

@@ -99,7 +99,7 @@ runs:
       run: |
         if [ -z "${{ inputs.path_to_claude_code_executable }}" ]; then
           echo "Installing Claude Code..."
-          curl -fsSL https://claude.ai/install.sh | bash -s 2.0.13
+          curl -fsSL https://claude.ai/install.sh | bash -s 2.0.25
         else
           echo "Using custom Claude Code executable: ${{ inputs.path_to_claude_code_executable }}"
           # Add the directory containing the custom executable to PATH

base-action/examples/issue-triage.yml

@@ -32,7 +32,7 @@ jobs:
                   "--rm",
                   "-e",
                   "GITHUB_PERSONAL_ACCESS_TOKEN",
-                  "ghcr.io/github/github-mcp-server:sha-7aced2b"
+                  "ghcr.io/github/github-mcp-server:sha-23fa0dd"
                 ],
                 "env": {
                   "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ secrets.GITHUB_TOKEN }}"

docs/faq.md

@@ -127,7 +127,7 @@ For performance, Claude uses shallow clones:
 If you need full history, you can configure this in your workflow before calling Claude in the `actions/checkout` step.
 
 ```
-- uses: actions/checkout@v4
+- uses: actions/checkout@v5
   depth: 0 # will fetch full repo history
 ```
 

docs/security.md

@@ -19,11 +19,22 @@
 
 ## GitHub App Permissions
 
-The [Claude Code GitHub app](https://github.com/apps/claude) requires these permissions:
+The [Claude Code GitHub app](https://github.com/apps/claude) requests the following permissions:
 
-- **Pull Requests**: Read and write to create PRs and push changes
-- **Issues**: Read and write to respond to issues
-- **Contents**: Read and write to modify repository files
+### Currently Used Permissions
+
+- **Contents** (Read & Write): For reading repository files and creating branches
+- **Pull Requests** (Read & Write): For reading PR data and creating/updating pull requests
+- **Issues** (Read & Write): For reading issue data and updating issue comments
+
+### Permissions for Future Features
+
+The following permissions are requested but not yet actively used. These will enable planned features in future releases:
+
+- **Discussions** (Read & Write): For interaction with GitHub Discussions
+- **Actions** (Read): For accessing workflow run data and logs
+- **Checks** (Read): For reading check run results
+- **Workflows** (Read & Write): For triggering and managing GitHub Actions workflows
 
 ## Commit Signing
 

docs/solutions.md

@@ -35,7 +35,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
@@ -89,7 +89,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
@@ -153,7 +153,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
@@ -211,7 +211,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
@@ -268,7 +268,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
@@ -344,7 +344,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -456,7 +456,7 @@ jobs:
       pull-requests: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           ref: ${{ github.event.pull_request.head.ref }}
           fetch-depth: 0
@@ -513,7 +513,7 @@ jobs:
       security-events: write
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

docs/usage.md

@@ -48,12 +48,12 @@ jobs:
 ## Inputs
 
 | Input                            | Description                                                                                                                                                                            | Required | Default       |
-| -------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------- | ------------- |
+| -------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------- | ------------- |
 | `anthropic_api_key`              | Anthropic API key (required for direct API, not needed for Bedrock/Vertex)                                                                                                             | No\*     | -             |
 | `claude_code_oauth_token`        | Claude Code OAuth token (alternative to anthropic_api_key)                                                                                                                             | No\*     | -             |
 | `prompt`                         | Instructions for Claude. Can be a direct prompt or custom template for automation workflows                                                                                            | No       | -             |
 | `track_progress`                 | Force tag mode with tracking comments. Only works with specific PR/issue events. Preserves GitHub context                                                                              | No       | `false`       |
-| `claude_args`                    | Additional arguments to pass directly to Claude CLI (e.g., `--max-turns 10 --model claude-4-0-sonnet-20250805`)                                                                | No       | ""            |
+| `claude_args`                    | Additional [arguments to pass directly to Claude CLI](https://docs.claude.com/en/docs/claude-code/cli-reference#cli-flags) (e.g., `--max-turns 10 --model claude-4-0-sonnet-20250805`) | No       | ""            |
 | `base_branch`                    | The base branch to use for creating new branches (e.g., 'main', 'develop')                                                                                                             | No       | -             |
 | `use_sticky_comment`             | Use just one comment to deliver PR comments (only applies for pull_request event workflows)                                                                                            | No       | `false`       |
 | `github_token`                   | GitHub token for Claude to operate with. **Only include this if you're connecting a custom GitHub app of your own!**                                                                   | No       | -             |

examples/ci-failure-auto-fix.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: ${{ github.event.workflow_run.head_branch }}
           fetch-depth: 0

examples/claude.yml

@@ -26,7 +26,7 @@ jobs:
       actions: read # Required for Claude to read CI results on PRs
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

examples/issue-deduplication.yml

@@ -15,7 +15,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

examples/issue-triage.yml

@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 

examples/manual-code-analysis.yml

@@ -23,7 +23,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 2 # Need at least 2 commits to analyze the latest
 

examples/pr-review-comprehensive.yml

@@ -16,7 +16,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

examples/pr-review-filtered-authors.yml

@@ -18,7 +18,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

examples/pr-review-filtered-paths.yml

@@ -19,7 +19,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 

src/create-prompt/index.ts

@@ -684,7 +684,7 @@ ${
 - Display the todo list as a checklist in the GitHub comment and mark things off as you go.
 - REPOSITORY SETUP INSTRUCTIONS: The repository's CLAUDE.md file(s) contain critical repo-specific setup instructions, development guidelines, and preferences. Always read and follow these files, particularly the root CLAUDE.md, as they provide essential context for working with the codebase effectively.
 - Use h3 headers (###) for section titles in your comments, not h1 headers (#).
-- Your comment must always include the job run link (and branch link if there is one) at the bottom.
+- Your comment must always include the job run link in the format "[View job run](${GITHUB_SERVER_URL}/${context.repository}/actions/runs/${process.env.GITHUB_RUN_ID})" at the bottom of your response (branch link if there is one should also be included there).
 
 CAPABILITIES AND LIMITATIONS:
 When users ask you to do something, be aware of what you can and cannot do. This section helps you understand how to respond when users request actions outside your scope.

src/mcp/install-mcp-server.ts

@@ -209,7 +209,7 @@ export async function prepareMcpConfig(
           "GITHUB_PERSONAL_ACCESS_TOKEN",
           "-e",
           "GITHUB_HOST",
-          "ghcr.io/github/github-mcp-server:sha-efef8ae", // https://github.com/github/github-mcp-server/releases/tag/v0.9.0
+          "ghcr.io/github/github-mcp-server:sha-23fa0dd", // https://github.com/github/github-mcp-server/releases/tag/v0.17.1
         ],
         env: {
           GITHUB_PERSONAL_ACCESS_TOKEN: githubToken,