# AI Agent Instructions: agentic-devtools Python Package

> Parent Instruction Chain
>
> 1. [Root global instructions](../../../.github/copilot-instructions.md)
> 2. [Scripts & Automation Navigation Hub](../../.github/copilot-instructions.md)
>
> [`copilot-instructions.md` Precedence Model](../../../docs/copilot-instructions-precedence-model.md)

## 1. Purpose

`agentic-devtools` is a pip-installable Python package that provides CLI commands for AI agents to interact with
Git, Azure DevOps, Jira, and other services. The design prioritizes **auto-approval** in VS Code by using:

- A generic `agdt-set key value` command (approve once, works for all keys)
- Parameterless action commands like `agdt-git-save-work`, `agdt-add-jira-comment`
- Native Python CLI handling of special characters and multiline content (no replacement tokens needed!)

### Copilot Chat Agents

Workflow steps can be started from VS Code Copilot Chat using `/agdt.<workflow>.<step>` commands.
Agents live in `.github/agents/` and prompts live in `.github/prompts/`, mirroring the
existing `speckit.*` pattern.

### Multi-Worktree Development

The package supports **multi-worktree development** using a single global pip/pipx install of `agentic-devtools` shared across all
worktrees. Each worktree has its own `.agdt/workflows/{identity}/{worktree_key}/state.json` file, so state is fully isolated between branches.

- **Single Global Install**: Install once with `pip install agentic-devtools` or `pipx install agentic-devtools`; all worktrees use the same installation
- **No Command Changes**: The same `agdt-*` commands work everywhere - entry points call implementations directly

### Background Task Architecture

**All action commands** spawn background tasks and return immediately:

- Commands like `agdt-git-save-work`, `agdt-add-jira-comment`, `agdt-create-pull-request` run in the background
- They return immediately with a task ID for tracking
- Results are written to output files in the workflow state directory when the task completes
- Use `agdt-task-status`, `agdt-task-log`, or `agdt-task-wait` to monitor progress
- The immediate console output tells the AI agent:
  1. What background task was triggered
  2. The task ID for status checking
  3. Where to find results when complete (output file path)

### ⚠️ CRITICAL: Testing Commands

**When working on `agentic-devtools`, ALWAYS use `agdt-test` commands - NEVER run pytest directly!**

```bash
# Full test suite (background, ~55 seconds for 2000+ tests)
agdt-test
agdt-task-wait

# Quick tests without coverage (background)
agdt-test-quick
agdt-task-wait

# Specific source file with 100% coverage requirement (background)
agdt-test-file --source-file agentic_devtools/state.py  # Auto-saves to state
agdt-task-wait

# Specific test - synchronous (simpler for quick checks)
agdt-test-pattern tests/test_jira_helpers.py::TestClassName -v
```

Why:

- Tests run as background tasks to prevent AI agents from thinking something went wrong
- Logs are captured properly in `.agdt/workflows/…/background-tasks/logs/`
- Direct pytest calls don't integrate with the background task system
- `agdt-test-file` shows coverage ONLY for the specified source file

See [Testing](#13-testing) for all test commands.

### ⚠️ CRITICAL: Run PR Checks Before Pushing

**A `.githooks/pre-push` hook automatically runs targeted checks before each push.** Ensure hooks are configured:

```bash
git config core.hooksPath .githooks
```

The pre-push hook runs fast, scoped checks on changed files only (~30s):

1. ruff format (auto-fix — aborts push if files were reformatted)
2. ruff check (lint)
3. markdownlint (on changed `.md` files)
4. Per-file 100% branch coverage
5. mypy type checking
6. Test structure validation (if test files changed)

**If the hook aborts the push**, fix the issues, stage and amend your commit, then push again.

For manual targeted checks without pushing:

```bash
bash scripts/targeted-checks.sh
```

For the full test suite (manual pre-merge validation):

```bash
bash scripts/run-pr-checks.sh --full
```

For quick auto-fixable lint issues:

```bash
ruff check --fix .
ruff format .
```

Then push again — the pre-push hook will re-validate.

### ⚠️ CRITICAL: Single Commit Per PR

**Every pull request MUST contain exactly one commit.** This is a hard policy, not a guideline.

- **NEVER use `git commit`** — always use `agdt-git-save-work`, which automatically amends when the branch has commits ahead of
  `main` (or `origin/main` when available). This enforces the single-commit policy: once you have one commit on the branch, all subsequent saves amend it.
- **NEVER create additional commits** on a feature branch — always amend and force-push
- Adding a second commit to a PR branch is a **policy violation**

```bash
# Correct: amend existing commit (agdt-git-save-work auto-detects amend vs new commit)
agdt-git-save-work

# WRONG: never do this
git commit -m "fix review feedback"   # ❌ creates a second commit (policy violation)
git commit --amend                    # ❌ wrong tool (use agdt-git-save-work)
```

Why this matters:

- **Clean git history** — one commit per PR = linear, readable history after squash-merge
- **Atomic changes** — each PR represents a single logical change
- **Easier reverts** — one commit = one revert if something goes wrong

### ⚠️ CRITICAL: Auto-Merge Label (`ai-auto-merge-allowed`)

**Before kicking off any AI agent session that will result in a PR being created, you MUST ask the user whether the `ai-auto-merge-allowed` label should be added to the PR.**

Rules for AI agents:

- **NEVER add `ai-auto-merge-allowed` to a PR unless you were explicitly instructed to do so** in the session instructions.
- When starting an agent session (e.g. `/agdt.address-copilot-review`, `agdt-initiate-*-workflow`, `agdt.pr-merge-manager`, or any other workflow that will result in a PR), **ask the user first**:
  > "Should the `ai-auto-merge-allowed` label be added to the PR? (This enables auto-merge via the AI PR loop once all checks pass and Copilot approves.)"
- If the user says yes, **include an explicit instruction in the agent's session prompt**: `"Add the 'ai-auto-merge-allowed' label to the PR after creating it."`
- If the user says no or does not answer, **do not add the label**.
- Repo workflows may auto-apply this label only when explicitly enabled (for example `SPECKIT_AUTO_MERGE_ALLOWED_LABEL == 'true'`); if not enabled, agents must treat it as not approved.
- Do not infer intent from context — only add the label when explicitly instructed.

### ⚠️ CRITICAL: Always Use agdt Commands

**AI agents MUST prefer `agdt-*` CLI commands over raw equivalents wherever support exists.**

Using raw commands (e.g., `git`, raw REST API calls, `pytest`) bypasses:

- The **background task system** — raw `git` commands stall agents; `agdt-git-save-work` runs in the background
- **Workflow integration** — `agdt-*` commands auto-advance workflow steps, update checklists, and manage state
- **Auto-approval benefits** — the `agdt-set` / `agdt-<action>` pattern allows VS Code to approve once for all keys
- **Dry-run safety** — `agdt-*` commands respect `dry_run` state; raw commands do not

#### Command Mapping

| Instead of... | Use... |
|---------------|--------|
| `git add . && git commit && git push` | `agdt-git-save-work` |
| `git commit --amend` | `agdt-git-save-work` (auto-detects amend) |
| `git push --force` | `agdt-git-force-push` |
| `git push -u origin <branch>` | `agdt-git-publish` |
| `pytest ...` | `agdt-test`, `agdt-test-file`, `agdt-test-pattern`, `agdt-test-quick` |
| Raw Azure DevOps REST API calls | `agdt-create-pull-request`, `agdt-add-pull-request-comment`, etc. |
| Raw Jira REST API calls | `agdt-add-jira-comment`, `agdt-get-jira-issue`, etc. |
| `gh issue create` (for this repo) | `agdt-create-agdt-feature-issue`, `agdt-create-agdt-bug-issue`, etc. |
| `gh pr view ... --json` | `agdt-gh-pr-state` |
| `gh pr checks` + `gh api check-suites` | `agdt-gh-pr-checks-status` |
| `gh api .../reviews` + GraphQL suppressed pagination | `agdt-gh-copilot-review-status` |
| `gh api ... actions/runs/{id}/rerun` | `agdt-gh-rerun-checks` |
| `gh api graphql` (thread pagination + `resolveReviewThread` mutation) | `agdt-gh-resolve-review-threads` |
| `gh pr review --approve` + manual verification | `agdt-gh-pr-approve` |
| `gh api .../requested_reviewers -X POST` | `agdt-gh-request-copilot-review` |
| Manual Phase 2 PR polling loop | `agdt-gh-pr-poll-ready` |
| `gh pr merge --rebase --delete-branch` + manual verification | `agdt-gh-pr-merge` |
| `gh api` loop for PR review comment replies | `agdt-gh-reply-to-review-comments` |

#### Exceptions — Raw Commands Still Required

> ⚠️ No agdt equivalent yet. Switch to agdt command when support is added.

| Raw command | Reason still needed |
|-------------|---------------------|
| `gh issue` / `gh pr` for repos other than agentic-devtools | No agdt support yet for general GitHub operations |
| `gh pr comment` for external repos | No agdt support yet for general GitHub PR comments |
| Other `gh` operations not listed in the command mapping above | No agdt equivalent exists |

### GitHub PR Actions (Synchronous)

| Command | Purpose | Required State / CLI Args |
|---------|---------|---------------------------|
| `agdt-gh-pr-state` | Fetch structured GitHub PR state | `--pr` (int) and optionally `--repo` (owner/repo); falls back to `github.pull_request_number` and `github.repo` state keys or git remote auto-detection |
| `agdt-gh-pr-poll-ready` | Poll PR until ready to merge or blocked | `--pr` or `github.pull_request_number`; optional `--repo`, `--poll-interval`, `--max-wait`, `--background`, `--rerun-stale-checks` |
| `agdt-gh-pr-approve` | Approve a GitHub PR with verification and retry | `--pr` (int) or `github.pull_request_number`; optional `--repo` (owner/repo), `--body` (approval comment) |
| `agdt-gh-pr-merge` | Merge a GitHub PR with verification and retry | `--pr` (int) or `github.pull_request_number`; optional `--repo` (owner/repo), `--strategy` (squash/merge/rebase, default rebase), `--no-delete-branch`; `--repo` falls back to `github.repo` state or git remote auto-detection |
| `agdt-gh-rerun-checks` | Re-run stale/failed GitHub Actions workflows | `--pr` (int) or `github.pull_request_number`; optional `--repo`, `--head-sha`, `--filter` (workflow name substring), `--include-cancelled` |
| `agdt-gh-request-copilot-review` | Request Copilot review with verification | `--pr` (int) or `github.pull_request_number`; optional `--repo` |
| `agdt-gh-reply-to-review-comments` | Post batch replies to PR review comments with verification | `--pr` (int) or `github.pull_request_number`; `--review-id` (int) or `github.copilot_review_id`; `--replies-file` (path to JSON); optional `--repo` |

**State keys written by `agdt-gh-pr-state`:**
`github.pull_request_number`, `github.repo`, `github.pr_state`,
`github.head_ref_oid`, `github.head_ref_oid_short`, `github.mergeable`,
`github.merge_state_status`, `github.is_draft`, `github.is_terminal`

**State keys written by `agdt-gh-pr-approve`:**
`github.pr_approval_verified` (bool), `github.pr_approval_review_id` (int or null)

**State keys written by `agdt-gh-pr-merge`:**
`github.pr_merged` (bool), `github.pr_merged_at` (ISO-8601 string or null),
`github.pr_merge_strategy` (string: squash/merge/rebase)

**State keys written by `agdt-gh-rerun-checks`:**
`github.rerun_checks_count` (int), `github.rerun_checks_failed_to_rerun` (int)

**State keys written by `agdt-gh-request-copilot-review`:**
`github.copilot_review_requested` (bool), `github.copilot_review_request_verified` (bool)

**State keys written by `agdt-gh-reply-to-review-comments`:**
`github.review_replies_total` (int), `github.review_replies_successful` (int),
`github.review_replies_failed` (int), `github.review_replies_verified` (bool)

**Usage:**

```bash
# With explicit args
agdt-gh-pr-state --pr 1115 --repo ayaiayorg/agentic-devtools

# With state (repo auto-detected from git remote)
agdt-set github.pull_request_number 1115
agdt-gh-pr-state
```

**`agdt-gh-pr-poll-ready` replaces the entire Phase 2 polling loop of the pr-merge-manager prompt.** It calls sibling Python functions directly in-process each iteration:

```bash
# Foreground (blocks until ready or blocked)
agdt-gh-pr-poll-ready --pr 1115 --repo owner/repo --poll-interval 60 --max-wait 600

# Background task mode
agdt-gh-pr-poll-ready --pr 1115 --background

# Disable stale check re-runs
agdt-gh-pr-poll-ready --pr 1115 --no-rerun-stale-checks
```

**Output:** Structured JSON to stdout with `ready`, `reason`, `actionRequired` fields.

**State keys written by `agdt-gh-pr-poll-ready`:** `github.pr_poll_ready_result`, `github.pr_poll_ready_action`.

## 2. Package Structure

```text
agentic_devtools/
├── __init__.py          # Package metadata
├── state.py             # JSON state management (single file: agdt-state.json)
├── file_locking.py      # Cross-platform file locking for state
├── task_state.py        # Background task state schema and CRUD
├── background_tasks.py  # Background task execution infrastructure
├── cli/
│   ├── __init__.py
│   ├── state.py         # Generic set/get/delete/clear/show commands
│   ├── azure_devops/    # Azure DevOps module (modular package)
│   │   ├── __init__.py  # Re-exports public API for backward compatibility
│   │   ├── config.py    # Constants + AzureDevOpsConfig dataclass
│   │   ├── auth.py      # PAT and auth header functions
│   │   ├── helpers.py   # Pure utility functions (no state reading)
│   │   ├── commands.py  # CLI commands with dry_run + state reading
│   │   ├── file_review_commands.py  # File-level review commands: approve, request-changes, suggestions, submit-review
│   │   ├── mark_reviewed.py         # Mark files as reviewed in Azure DevOps
│   │   ├── review_commands.py       # PR review workflow entry point
│   │   ├── review_state.py          # Review state schema & CRUD
│   │   ├── review_templates.py      # Markdown template engine for summaries
│   │   ├── review_scaffold.py       # Upfront thread scaffolding
│   │   ├── status_cascade.py        # Status derivation & cascade logic
│   │   ├── review_attribution.py    # AI model attribution & commit tagging
│   │   ├── review_models_config.py  # Multi-model review configuration
│   │   ├── verdict_protocol.py      # Verdict recording & consolidation logic
│   │   ├── suggestion_verification.py # Suggestion verification for re-reviews
│   │   └── suggestion_commands.py   # Confirm/reject suggestion CLI commands
│   ├── git/             # Git workflow commands (package)
│   │   ├── __init__.py  # Command exports
│   │   ├── core.py      # State helpers, git execution, temp files
│   │   ├── operations.py # Individual git operations
│   │   └── commands.py  # CLI entry points
│   ├── github/          # GitHub CLI commands (package)
│   │   ├── __init__.py  # Command exports
│   │   ├── state_helpers.py  # issue.* namespace helpers
│   │   ├── repo_resolution.py # Shared owner/repo resolution for agdt-gh-* commands
│   │   ├── request_copilot_review.py # Request Copilot review with verification
│   │   ├── issue_commands.py # Synchronous issue creation commands
│   │   ├── async_commands.py # Background/async command wrappers + CLI entry points
│   │   └── review_reply.py   # Batch reply to PR review comments with verification
│   ├── jira/            # Jira commands (package)
│   │   ├── __init__.py  # Command exports
│   │   ├── config.py    # Jira configuration and auth
│   │   ├── commands.py  # Synchronous CLI entry points
│   │   ├── update_commands.py # Issue update command
│   │   └── async_commands.py  # Background/async command wrappers
│   └── tasks/           # Background task monitoring (package)
│       ├── __init__.py  # Command exports
│       └── commands.py  # Task monitoring CLI commands
├── prompts/             # Prompt template system (package)
│   ├── __init__.py      # Package exports
│   └── loader.py        # Template loading, validation, substitution
└── pyproject.toml       # Package config with entry points
```

### Module Responsibilities

| Module | Responsibility |
|--------|---------------|
| `azure_devops/config.py` | Constants (`DEFAULT_ORGANIZATION`, `APPROVAL_SENTINEL`, etc.) and `AzureDevOpsConfig` dataclass |
| `azure_devops/auth.py` | `get_pat()` and `get_auth_headers()` for Azure DevOps authentication |
| `azure_devops/helpers.py` | Pure utility functions: `build_thread_context`, `convert_to_pull_request_title`, `format_approval_content`, etc. |
| `azure_devops/commands.py` | CLI entry points: `reply_to_pull_request_thread`, `add_pull_request_comment`, `create_pull_request`, etc. |
| `azure_devops/file_review_commands.py` | File-level review: `approve_file`, `request_changes`, `request_changes_with_suggestion`, `submit_file_review` |
| `azure_devops/mark_reviewed.py` | Mark files as reviewed in Azure DevOps: updates Reviewers API and Contribution API for UI display |
| `azure_devops/review_commands.py` | PR review workflow: `review_pull_request`, prompt generation, Jira integration |
| `azure_devops/__init__.py` | Re-exports all public API for backward compatibility (`from agentic_devtools.cli.azure_devops import reply_to_pr_thread`) |
| `azure_devops/review_state.py` | Review state schema (`ReviewState`, `FileEntry`, `SuggestionEntry`, `ReviewSession`) and CRUD (`load_review_state`, `save_review_state`, `update_file_status`) for `review-state.json` |
| `azure_devops/review_templates.py` | Markdown template engine: `render_file_summary`, `render_overall_summary`, `build_discussion_url` for review comment rendering |
| `azure_devops/review_scaffold.py` | Upfront thread scaffolding: creates file/overall summary threads during `agdt-review-pull-request`, with idempotent re-scaffolding on new commits |
| `azure_devops/status_cascade.py` | Status derivation rules (`compute_aggregate_status`) and overall PR summary PATCH operations (`cascade_status_update`, `execute_cascade`) derived directly from file statuses (no folder-level threads) |
| `azure_devops/review_attribution.py` | AI model attribution: model icons, commit hash links, emoji status formatting |
| `azure_devops/review_models_config.py` | Multi-model review configuration: `ReviewModelsConfig`, base/override config file loading from `.agdt/config/` |
| `azure_devops/verdict_protocol.py` | Verdict recording and consolidation trigger logic: `record_verdict`, `compute_file_effective_status`, `evaluate_consolidation_need` |
| `azure_devops/suggestion_verification.py` | Suggestion verification for re-reviews: `verify_previous_suggestions`, `SuggestionVerificationResult` |
| `azure_devops/suggestion_commands.py` | Confirm/reject suggestion CLI commands: `confirm_suggestion_addressed`, `reject_suggestion_resolution` |
| `git/core.py` | State helpers, git command execution, temp file handling |
| `git/operations.py` | Individual git operations (stage, commit, push, etc.) and smart amend detection |
| `git/commands.py` | CLI entry points: `agdt-git-save-work` (auto-detects amend), `agdt-git-stage`, `agdt-git-push`, etc. |
| `github/__init__.py` | Re-exports public API for `agdt-create-agdt-*` commands |
| `github/state_helpers.py` | `get_issue_value()` and `set_issue_value()` for the `issue.*` state namespace |
| `github/issue_commands.py` | Sync implementations: `create_agdt_issue`, `create_agdt_bug_issue`, `create_agdt_feature_issue`, `create_agdt_documentation_issue`, `create_agdt_task_issue` |
| `github/async_commands.py` | Async wrappers (background tasks) and argparse CLI entry points for all `agdt-create-agdt-*` commands |
| `github/repo_resolution.py` | `resolve_github_repo()` for resolving `owner/repo` from CLI args or git remote |
| `github/pr_checks_status.py` | Dual-source CI check verification: `get_pr_checks_status()`, `pr_checks_status_command()` |
| `prompts/loader.py` | Template loading, variable extraction, validation, substitution, and output saving |
| `cli/workflows/base.py` | Base workflow utilities: `validate_required_state`, `initiate_workflow`, `advance_workflow_step` |
| `cli/workflows/commands.py` | Workflow initiation CLI commands for each workflow type |
| `cli/workflows/preflight.py` | Pre-flight checks for work-on-jira-issue: worktree/branch validation |
| `cli/workflows/advancement.py` | Auto-advancement helpers called by other commands to progress workflows |

## 3. State Management Pattern

All state is stored in a single JSON file (`.agdt/workflows/{identity}/{worktree_key}/state.json`):

```python
from agentic_devtools.state import get_value, set_value, load_state

# Set values
set_value("pr_id", 23046)
set_value("content", "My reply message")

# Get values
pr_id = get_value("pr_id")
content = get_value("content")

# Load entire state
state = load_state()  # Returns dict
```

### Workflow State

Workflow state is stored separately under the `_workflow` key and managed through dedicated functions:

```python
from agentic_devtools.state import (
    get_workflow_state, set_workflow_state, clear_workflow_state,
    is_workflow_active, update_workflow_step, update_workflow_context
)

# Set workflow state
set_workflow_state(
    name="pull-request-review",
    status="active",
    step="initiate",
    context={"pull_request_id": "123"}
)

# Check if a workflow is active
if is_workflow_active():
    workflow = get_workflow_state()
    print(f"Active: {workflow['name']} at step {workflow['step']}")

# Update workflow progress
update_workflow_step("reviewing")
update_workflow_context(files_reviewed=5)

# Clear when done
clear_workflow_state()
```

### Workflow Transition Behavior

Workflows advance through steps via event-driven transitions. The transition behavior depends on the `auto_advance` flag and `required_tasks`:

1. **Immediate Advancement** (auto_advance=True, no required_tasks):
   - The workflow step changes immediately
   - The next step's prompt is rendered and printed to the console
   - Examples: `CHECKLIST_CREATED`, `CHECKLIST_COMPLETE`, `JIRA_COMMENT_ADDED`

2. **Deferred Advancement** (auto_advance=True, has required_tasks):
   - A `pending_transition` is recorded in the workflow context
   - The step changes when `agdt-get-next-workflow-prompt` is called AND the background tasks complete
   - Examples: `GIT_COMMIT_CREATED` (waits for agdt-git-commit task)

3. **Manual Advancement** (auto_advance=False):
   - Requires explicit `agdt-advance-workflow` command
   - Used for steps that need human confirmation

When a transition fires immediately, the output looks like:

```text
================================================================================
WORKFLOW ADVANCED: work-on-jira-issue
NEW STEP: implementation-review
================================================================================

# Work on Jira Issue - Implementation Review Step
...
```

### Issue Key (Provider-Agnostic)

The top-level `issue_key` is the canonical, provider-agnostic issue identifier. It supports
both Jira keys (`PROJECT-1234`) and GitHub issue numbers (`#42`, `42`):

```bash
# Primary way to set the current issue identifier (provider-agnostic)
agdt-set issue_key 42

# Jira-specific legacy key (backward compatible — continues to work)
agdt-set jira.issue_key PROJECT-1234
```

Numeric issue IDs (e.g., `42`) are JSON-parsed as integers by `agdt-set`.
Read paths that resolve the current issue key normalize that value to its
string representation, so `agdt-set issue_key 42` and `agdt-set issue_key "42"`
produce equivalent behavior.

All core functions that resolve an issue key check `issue_key` first, then fall back to
`jira.issue_key`. Both keys can coexist with different values — setting one does **not**
clear the other. Both are context-switching keys — setting either one clears
`pull_request_id`, and setting `pull_request_id` clears both `issue_key` and `jira.issue_key`.

**Resolution priority** (used by `_get_issue_key_from_state`, `resolve_worktree_key`, etc.):

1. `issue_key` (top-level, provider-agnostic)
2. `jira.issue_key` (legacy Jira-specific key)
3. Workflow context `jira_issue_key` (for active workflows)
4. `pull_request_id` (fallback used by `resolve_worktree_key` when no issue key is set)

### Jira Namespace

Jira commands use keys prefixed with `jira.`:

```bash
agdt-set jira.issue_key PROJECT-1234
agdt-set jira.comment "My comment"
```

## 4. CLI Commands

### State Management

| Command | Purpose | Example |
|---------|---------|---------|
| `agdt-set` | Set any key-value | `agdt-set pull_request_id 23046` |
| `agdt-get` | Get a value | `agdt-get content` |
| `agdt-delete` | Remove a key | `agdt-delete thread_id` |
| `agdt-clear` | Clear all state | `agdt-clear` |
| `agdt-show` | Show all state | `agdt-show` |

### Azure DevOps Actions (Background Tasks)

All action commands that mutate state or perform API calls spawn background tasks and return immediately with a task ID for tracking.

| Command | Purpose | Required State / CLI Args |
|---------|---------|---------------------------|
| `agdt-add-pull-request-comment` | Add new PR comment | pull_request_id, content |
| `agdt-approve-pull-request` | Approve PR with sentinel banner | pull_request_id, content |
| `agdt-create-pull-request` | Create a new pull request | source_branch, title OR `--source-branch`, `--title`, `--description` |
| `agdt-reply-to-pull-request-thread` | Reply to PR thread | pull_request_id, thread_id, content |
| `agdt-resolve-thread` | Resolve a PR thread | pull_request_id, thread_id |
| `agdt-mark-pull-request-draft` | Mark PR as draft | pull_request_id |
| `agdt-publish-pull-request` | Publish draft PR | pull_request_id |
| `agdt-run-e2e-tests` | Trigger E2E test pipeline | (pipeline params) |
| `agdt-run-wb-patch` | Trigger workbench patch pipeline | (pipeline params) |
| `agdt-review-pull-request` | Start PR review workflow | (optional) pull_request_id, jira.issue_key |

**Create Pull Request CLI Parameter Support:**

```bash
# Option A: With CLI parameters (explicit)
agdt-create-pull-request --source-branch "feature/PROJECT-1234/new-feature" --title "feat([#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): add new feature" --description "Description here"

# Option B: Parameterless (uses current state)
# Check current values: agdt-get source_branch, agdt-get title
agdt-create-pull-request
```

### Azure DevOps Query Commands (Background Tasks)

Query commands also spawn background tasks - results are written to output files:

| Command | Purpose | Required State | Output File |
|---------|---------|----------------|-------------|
| `agdt-get-pull-request-threads` | Get all PR comment threads | pull_request_id | `temp/pr-threads-{pr_id}.json` |
| `agdt-get-pull-request-details` | Get full PR details (diff, threads, iterations) | pull_request_id | `temp/pr-details-{pr_id}.json` |
| `agdt-get-run-details` | Get pipeline/build run details | run_id | `temp/run-details-{run_id}.json` |

### Pull Request Review Commands (Background Tasks)

| Command | Purpose | Required State / CLI Args |
|---------|---------|---------------------------|
| `agdt-review-pull-request` | Start PR review workflow | (optional) pull_request_id or jira.issue_key |
| `agdt-approve-file` | Approve a file during review | pull_request_id, file_review.file_path, file_review.summary OR `--file-path`, `--summary`, `--pull-request-id` |
| `agdt-request-changes` | Request changes on a file | pull_request_id, file_review.file_path, file_review.summary, file_review.suggestions OR `--file-path`, `--summary`, `--suggestions`, `--pull-request-id` |
| `agdt-request-changes-with-suggestion` | Request changes with structured code suggestions | pull_request_id, file_review.file_path, file_review.summary, file_review.suggestions (each suggestion must include `replacement_code`) OR `--file-path`, `--summary`, `--suggestions`, `--pull-request-id` |
| `agdt-mark-file-reviewed` | Mark a file as reviewed (standalone) | pull_request_id, file_review.file_path |
| `agdt-submit-file-review` | Submit batched file review | pull_request_id |

**File Review CLI Parameter Support:**

File review commands accept optional CLI arguments that override state values:

```bash
# Option A: With CLI parameters (explicit, self-documenting)
agdt-approve-file --file-path "src/app/component.ts" --summary "LGTM - clean implementation"
agdt-request-changes --file-path "src/app/service.ts" --summary "Missing null check" --suggestions '[{"line": 42, "severity": "high", "content": "Missing null check"}]'
agdt-request-changes-with-suggestion --file-path "src/utils.ts" --summary "Null handling needs improvement." --suggestions '[{"line": 15, "severity": "high", "content": "Use null-coalescing operator", "replacement_code": "const value = x ?? defaultValue;"}]'

# Option B: Parameterless (uses current state)
# Check current values: agdt-get file_review.file_path, agdt-get file_review.summary, agdt-get file_review.suggestions
agdt-approve-file
agdt-request-changes
```

**Review Command Behavior:**

All file review commands automatically:

1. Post the review comment (runs as background task)
2. Mark the file as reviewed in Azure DevOps (visible as "viewed" eye icon in PR UI)
3. Update the hierarchical review threads in Azure DevOps via PATCH requests (file, folder, and overall summary threads), then save the refreshed state to `review-state.json`
4. Print next steps (continue with next file or advance to summary step)

### GitHub PR CI Checks (Synchronous)

These commands interact with GitHub PRs via the `gh` CLI and return results directly (not background tasks).

| Command | Purpose | Required State / CLI Args |
|---------|---------|---------------------------|
| `agdt-gh-pr-checks-status` | Dual-source CI check verification | `--pr` or `github.pull_request_number`; `--repo` or git remote; optional `--head-sha` or `github.head_ref_oid` |

**`agdt-gh-pr-checks-status`** performs dual verification:

1. Fetches structured check results via `gh pr checks --json`
2. Verifies check-suite completion via `gh api` check-suites endpoint (when `head_sha` is available)

State keys written: `github.pr_checks_status`, `github.pr_checks_failed`, `github.pr_checks_pending`.

```bash
# With CLI parameters
agdt-gh-pr-checks-status --pr 1115 --repo ayaiayorg/agentic-devtools --head-sha abc123

# Using state (set via agdt-set)
agdt-gh-pr-checks-status
```

### GitHub PR Analysis (Synchronous)

| Command | Purpose | Required State / CLI Args |
|---------|---------|---------------------------|
| `agdt-gh-copilot-review-status` | Analyze Copilot review status for a PR | `github.pull_request_number`, `github.head_ref_oid` OR `--pr`, `--head-sha`; optional `github.repo` / `--repo` (auto-detected from git remote if omitted) |

**State Keys Written:**

- `github.copilot_review_status` — status string (`clean`, `no-review`, `has-feedback`, `changes-requested`, `unknown-state`)
- `github.copilot_review_id` — numeric review ID (or `null`)
- `github.copilot_review_node_id` — GraphQL node ID (or `null`)
- `github.copilot_review_url` — review URL (or `null`)

### Git Workflow Actions (Background Tasks)

All Git workflow commands spawn background tasks:

| Command | Purpose | Required State |
|---------|---------|----------------|
| `agdt-git-save-work` | Stage, commit/amend, publish/force-push | commit_message |
| `agdt-git-stage` | Stage all changes | (none) |
| `agdt-git-push` | Push to origin | (none) |
| `agdt-git-force-push` | Force push to origin | (none) |
| `agdt-git-publish` | Publish branch upstream | (none) |

**Smart Commit Detection:**
The `agdt-git-save-work` command automatically detects whether to create a new commit or amend:

- If branch has commits ahead of `origin/main` AND last commit contains current issue key → **amend + force push**
- Otherwise → **new commit + publish**

**Checklist Integration:**
Use `--completed` to mark checklist items during commit:

```bash
agdt-git-save-work --completed 1 2 3  # Marks items 1, 2, 3 complete before committing
```

**Optional CLI flags:**

- `--dry-run` - Preview operations without executing
- `--skip-stage` - Skip the staging step
- `--skip-push` - Skip the push step
- `--skip-rebase` - Skip the fetch/rebase onto main step

```bash
agdt-git-save-work --dry-run
agdt-git-save-work --skip-stage --skip-push
agdt-set commit_message "feat([#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): my change

[#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)"
agdt-git-save-work --skip-push
```

**Optional Git state keys:**

- `dry_run` - Preview operations without executing
- `skip_stage` - Skip the staging step
- `skip_push` - Skip the push step
- `skip_publish` - Skip branch publish after initial commit

### Jira Actions (Background Tasks)

All Jira action commands that mutate state spawn background tasks:

| Command | Purpose | Required State / CLI Args |
|---------|---------|---------------------------|
| `agdt-add-jira-comment` | Add comment to issue | `jira.issue_key`, `jira.comment` OR `--jira-comment`, `--jira-issue-key` |
| `agdt-update-jira-issue` | Update issue fields | jira.issue_key, plus field keys |
| `agdt-create-epic` | Create a new epic | jira.project_key, jira.summary, jira.epic_name, jira.role, jira.desired_outcome, jira.benefit |
| `agdt-create-issue` | Create a new issue | jira.project_key, jira.summary, jira.description (or role/outcome/benefit) |
| `agdt-create-subtask` | Create a subtask | jira.parent_key, jira.summary, jira.description |

**CLI Parameter Support:**
Some commands accept optional CLI arguments that override state values:

- `agdt-add-jira-comment --jira-comment "..." [--jira-issue-key KEY]` - Comment text and issue key can be passed directly
- When CLI args are provided, they are stored in state before execution

**Documentation Pattern for Commands with Optional Parameters:**

When documenting commands that support both CLI parameters and parameterless execution, show both options:

```bash
# Option A: With CLI parameters (explicit)
agdt-add-jira-comment --jira-comment "Your comment text here"

# Option B: Parameterless (uses current state)
# Current jira.issue_key: run `agdt-get jira.issue_key` to check
# Current jira.comment: run `agdt-get jira.comment` to check
agdt-add-jira-comment
```

This pattern:

1. Shows CLI parameters first for explicit, self-documenting usage
2. Shows parameterless alternative that uses current state values
3. Indicates how to check current state values before running parameterless

### Jira Role Management (Background Tasks)

| Command | Purpose | Required State |
|---------|---------|----------------|
| `agdt-list-project-roles` | List project roles | jira.project_key |
| `agdt-get-project-role-details` | Get role details | jira.project_key, jira.role_id |
| `agdt-add-users-to-project-role` | Add users to role | jira.project_key, jira.role_id, jira.usernames |
| `agdt-add-users-to-project-role-batch` | Batch add users | jira.project_key, jira.role_id, jira.usernames |
| `agdt-find-role-id-by-name` | Find role ID | jira.project_key, jira.role_name |
| `agdt-check-user-exists` | Check if user exists | jira.username |
| `agdt-check-users-exist` | Check multiple users | jira.usernames |

### Jira Query Commands (Background Tasks)

Jira query commands also spawn background tasks - results are written to output files:

| Command | Purpose | Required State | Output File |
|---------|---------|----------------|-------------|
| `agdt-get-jira-issue` | Get issue details | jira.issue_key | `temp/temp-get-issue-details-response.json` |
| `agdt-parse-jira-error-report` | Parse error report | (file input) | `temp/jira-error-report.json` |

**`agdt-get-jira-issue` Features:**

- **Automatic subtask detection**: Checks `issuetype.subtask` field
- **Automatic parent retrieval**: Fetches parent issue for subtasks → `temp/temp-get-parent-issue-details-response.json`
- **Automatic epic retrieval**: Fetches linked epic via `customfield_10008` → `temp/temp-get-epic-details-response.json`
- **Metadata references in state**: Stores file locations and timestamps, NOT full JSON:
  - `jira.issue_details` → `{location, retrievalTimestamp}`
  - `jira.parent_issue_details` → `{location, key, retrievalTimestamp}` (if subtask)
  - `jira.epic_details` → `{location, key, retrievalTimestamp}` (if epic linked)
- **Console output**: Prints formatted issue details including parent/epic info

**Update Issue State Keys:**

- `jira.summary` - New summary text
- `jira.description` - New description text
- `jira.labels` - Comma-separated labels (replaces existing)
- `jira.labels_add` - Comma-separated labels to add
- `jira.labels_remove` - Comma-separated labels to remove
- `jira.assignee` - Username to assign (empty string to unassign)
- `jira.priority` - Priority name (e.g., "High", "Medium", "Low")
- `jira.custom_fields` - JSON object of custom field IDs to values

### Background Task Management

| Command | Purpose | Required State |
|---------|---------|----------------|
| `agdt-tasks` | List all background tasks | (none) |
| `agdt-task-status` | Show detailed task status | background.task_id |
| `agdt-task-log` | Display task output log | background.task_id |
| `agdt-task-wait` | Wait for task completion | background.task_id |
| `agdt-tasks-clean` | Clean up expired tasks | (none) |

**Optional Background Task State Keys:**

- `background.task_id` - Task ID to query/wait for
- `background.timeout` - Wait timeout in seconds (default: 300)
- `background.poll_interval` - Poll interval in seconds (default: 2)
- `background.log_lines` - Number of log lines to show (negative for tail)
- `background.expiry_hours` - Hours before tasks expire (default: 24)

**Background Task Pattern:**

Action commands spawn background processes and return immediately:

```bash
# Start background operation
agdt-set jira.issue_key PROJECT-1234
agdt-set jira.comment "Processing complete"
agdt-add-jira-comment
# Output: Background task started: <task-id>

# Monitor the task
agdt-set background.task_id <task-id>
agdt-task-status   # Check current status
agdt-task-log      # View output log
agdt-task-wait     # Wait for completion
```

### GitHub PR Thread Resolution (Synchronous)

These commands interact with GitHub PRs via the `gh` CLI and GraphQL. They run **synchronously** (not as background tasks) and print structured JSON to stdout.

| Command | Purpose | Required CLI Args / State |
|---------|---------|---------------------------|
| `agdt-gh-resolve-review-threads` | Resolve PR review threads via GraphQL | `--pr` or `github.pull_request_number`; `--review-id` or `github.copilot_review_id` or `--comment-ids` |

**`agdt-gh-resolve-review-threads` Usage:**

```bash
# Resolve all threads for a specific review
agdt-gh-resolve-review-threads --pr 1115 --repo ayaiayorg/agentic-devtools --review-id 4066913338

# Resolve specific comment IDs only
agdt-gh-resolve-review-threads --pr 1115 --comment-ids 12345,12346,12347
```

**State keys written:** `github.threads_resolved_count`, `github.threads_failed_count`, `github.threads_already_resolved_count`, `github.threads_resolution_verified`.

### Testing Actions

**⚠️ CRITICAL FOR AI AGENTS: ALWAYS use these agdt-test commands, NEVER run pytest directly!**

These commands run tests in BACKGROUND TASKS and return immediately with a task ID.
The test suite has 2000+ tests and takes ~55 seconds - running synchronously causes
AI agents to think something went wrong and restart tests multiple times.

| Command | Purpose | Required State |
|---------|---------|----------------|
| `agdt-test` | Run full test suite with coverage (~55s) | (none) |
| `agdt-test-quick` | Run tests without coverage (faster) | (none) |
| `agdt-test-file --source-file <path>` | Run tests for a specific source file with 100% coverage | (none - uses `--source-file` param) |
| `agdt-test-pattern <args>` | Run specific tests (SYNCHRONOUS) | (none - takes args) |

**Basic workflow (full test suite):**

```bash
# Run tests in background
agdt-test

# Wait for completion (REQUIRED - do not skip!)
agdt-task-wait
```

**Running tests for a specific source file (with focused coverage):**

```bash
# Specify source file via --source-file (auto-saved to state for future runs)
agdt-test-file --source-file agentic_devtools/state.py
agdt-task-wait
```

This is ideal when working on a single module and wanting to ensure full test coverage.
The command:

- Infers the test file from the source file name (e.g., `state.py` → `test_state.py`)
- Shows coverage ONLY for the specified source file (not the entire codebase)
- Requires 100% coverage for the target file to pass
- Auto-saves `--source-file` to state, so subsequent runs can omit the parameter

**Running specific test classes or methods (synchronous):**

```bash
# Test a specific class
agdt-test-pattern tests/test_jira_helpers.py::TestEnsureJiraPem -v

# Test a specific method
agdt-test-pattern "tests/test_state.py::TestWorkflowState::test_set_and_get_workflow_state" -v
```

**When to use which command:**

- `agdt-test` - Full suite validation before committing (required!)
- `agdt-test-quick` - Full suite without coverage for faster iteration
- `agdt-test-file` - Background execution for specific file/pattern (use when you want to check other things while tests run)
- `agdt-test-pattern` - Synchronous execution when you need immediate results from a specific test

**DO NOT:**

- Run `pytest` directly
- Run multiple test commands in parallel
- Assume tests failed if command returns quickly (they run in background)

### Workflow Management

| Command | Purpose | Required State |
|---------|---------|----------------|
| `agdt-get-workflow` | Display current workflow state | (none) |
| `agdt-clear-workflow` | Clear workflow state | (none) |
| `agdt-create-checklist` | Create checklist from CLI args | (none - takes args) |
| `agdt-update-checklist` | Update checklist items | (checklist in workflow) |
| `agdt-show-checklist` | Display current checklist | (checklist in workflow) |

### Workflow Initiation Commands

These commands initiate a workflow, loading and rendering the appropriate prompt template:

| Command | Purpose | Required Parameters |
|---------|---------|---------------------|
| `agdt-initiate-pull-request-review-workflow` | Start PR review workflow | `--pull-request-id` or `--issue-key`; optional `--interactive false` for pipeline mode |
| `agdt-initiate-work-on-jira-issue-workflow` | Start work on Jira issue | `--issue-key` |
| `agdt-initiate-create-jira-issue-workflow` | Start create issue workflow | `--project-key` |
| `agdt-initiate-create-jira-epic-workflow` | Start create epic workflow | `--project-key` |
| `agdt-initiate-create-jira-subtask-workflow` | Start create subtask workflow | `--parent-key` |
| `agdt-initiate-update-jira-issue-workflow` | Start update issue workflow | `--issue-key` |
| `agdt-initiate-apply-pr-suggestions-workflow` | Apply PR review suggestions | `--pull-request-id` |
| `agdt-advance-workflow` | Advance to next workflow step | (active workflow) |

**Workflow Command Behavior:**

1. Validates required state keys are present
2. Collects variables from state (both required and optional)
3. Loads the appropriate prompt template (override if exists, else default)
4. Validates override template doesn't introduce new variables
5. Substitutes variables into the template
6. Saves the rendered prompt to `temp-<workflow>-<step>-prompt.md` in the workflow state directory
7. Logs the prompt to console with a notice of where it was saved
8. Updates workflow state (name, status=active, step, context)

### Work-on-Jira-Issue Workflow (State Machine)

The `agdt-initiate-work-on-jira-issue-workflow` uses an enhanced state-machine approach:

**Pre-flight Checks:**

1. Validates that the current folder contains the issue key (case-insensitive)
2. Validates that the current git branch contains the issue key
3. If either check fails → outputs setup instructions with worktree/branch commands

**Steps:**

1. **setup** - If pre-flight fails: instructions to create worktree and branch
2. **retrieve** - Auto-fetches Jira issue details via `agdt-get-jira-issue`
3. **planning** - Analyze issue and post plan comment to Jira
4. **checklist-creation** - Create implementation checklist based on plan
5. **implementation** - Code changes, tests, documentation (with checklist tracking)
6. **implementation-review** - Review completed checklist before verification
7. **verification** - Run tests and quality gates
8. **commit** - Stage and commit changes
9. **pull-request** - Create PR
10. **completion** - Post final Jira comment

**Automatic Workflow Advancement:**

- `agdt-add-jira-comment` advances from `planning` → `checklist-creation`
- `agdt-create-checklist` advances from `checklist-creation` → `implementation`
- When all checklist items are complete → advances to `implementation-review`
- `agdt-git-save-work` advances from `commit` → `pull-request`
- `agdt-create-pull-request` advances from `pull-request` → `completion`

### Checklist Management Commands

| Command | Purpose | Required State |
|---------|---------|----------------|
| `agdt-create-checklist` | Create checklist from CLI args | (none - takes args) |
| `agdt-update-checklist` | Update checklist items | (checklist in workflow) |
| `agdt-show-checklist` | Display current checklist | (checklist in workflow) |

**Usage:**

```bash
# Create checklist
agdt-create-checklist "Implement domain model" "Add tests" "Update docs"

# Mark items as complete
agdt-update-checklist --completed 1 2

# View checklist
agdt-show-checklist

# Mark items complete during commit
agdt-git-save-work --completed 1 2 3
```

**Manual Advancement:**

```bash
# Advance to a specific step
agdt-advance-workflow implementation
agdt-advance-workflow verification
agdt-advance-workflow commit

# View current step
agdt-get-workflow
```

**Usage Examples:**

```bash
# Start work on a Jira issue
agdt-set jira.issue_key PROJECT-1234
agdt-initiate-work-on-jira-issue-workflow
# If pre-flight fails: shows worktree/branch setup instructions
# If pre-flight passes: auto-fetches issue and shows planning prompt

# Check current workflow
agdt-get-workflow
# Output: name=work-on-jira-issue, status=in-progress, step=planning

# Post plan comment (auto-advances to implementation)
agdt-set jira.comment "h4. Plan..."
agdt-add-jira-comment

# Advance manually when needed
agdt-advance-workflow verification

# Clear workflow when done
agdt-clear-workflow
```

**Usage examples:**

```bash
# ⚠️ ALWAYS use agdt-test commands, NEVER pytest directly!

# Full suite with coverage (runs in background, ~55 seconds)
agdt-test
agdt-task-wait   # REQUIRED: Wait for completion

# Quick run without coverage (runs in background)
agdt-test-quick
agdt-task-wait

# Specific file, class, or test via CLI argument (runs synchronously)
agdt-test-pattern tests/test_jira_helpers.py::TestEnsureJiraPem
agdt-test-pattern tests/test_jira_helpers.py::TestEnsureJiraPem::test_returns_existing_pem_path

# Test a specific source file with 100% coverage (runs in background)
agdt-test-file --source-file agentic_devtools/state.py  # Auto-saved to state
agdt-task-wait   # REQUIRED: Wait for completion
```

## 5. Key Design Decisions

### No Replacement Tokens

Unlike PowerShell, Python CLI handles special characters natively:

```bash
# This just works - no token replacement needed!
agdt-set content "Code with (parentheses) and [brackets]"
```

### No Multi-line Builder

Python preserves multiline strings directly:

```bash
agdt-set content "Line 1
Line 2
Line 3"
```

### Generic Setter Pattern

The `agdt-set` command accepts any key, so AI agents only need to approve it once:

```bash
agdt-set pr_id 12345       # Same command pattern
agdt-set thread_id 67890   # Same command pattern
agdt-set content "text"    # Same command pattern
```

### ⚠️ Security: `run_safe` and User-Controlled Content

When calling `run_safe` with a list of arguments that includes
**user-controlled text** (e.g., issue titles, PR body content,
commit messages, file paths from state),
always pass **`shell=False`** explicitly:

```python
# ✅ CORRECT — user-controlled text, shell=False prevents env-var expansion on Windows
result = run_safe(["gh", "issue", "create", "--title", title, "--body", body],
                  capture_output=True, text=True, shell=False)

# ❌ DANGEROUS — default shell=None uses shell=True on Windows, allowing cmd.exe to
#    expand %VARIABLE% patterns (e.g., %GITHUB_TOKEN%) in user-supplied text
result = run_safe(["gh", "issue", "create", "--title", title, "--body", body],
                  capture_output=True, text=True)
```

Only omit `shell=False` (or pass `shell=True` explicitly) for commands
known to be **`.cmd`/`.bat` batch scripts** on Windows, such as `az`
(Azure CLI) and `npm`. Proper executables like `gh`, `git`, `code`,
`python`, etc. must always be called with `shell=False` when argument
values contain user-supplied data.

For **`.cmd`/`.bat` batch scripts** like `az`, rely on `run_safe`'s
Windows-only default (`shell=None`) rather than passing `shell=True`
explicitly. This way, Linux/macOS runs use `shell=False` (more secure),
and Windows still gets `shell=True` automatically for batch scripts:

```python
# ✅ CORRECT — shell=None default: shell=True on Windows only, shell=False elsewhere
result = run_safe(["az", "repos", "pr", "show", "--id", str(pr_id)],
                  capture_output=True, text=True)

# ❌ AVOID — forces shell=True on all platforms, expanding attack surface on Linux/macOS
result = run_safe(["az", "repos", "pr", "show", "--id", str(pr_id)],
                  capture_output=True, text=True, shell=True)
```

## 6. Prompt Template System

Workflow commands use a template system for generating prompts:

### Template Location

- **Default templates**: `agentic_devtools/prompts/default-<step>-<workflow>-prompt.md`
- **Override templates**: `agentic_devtools/prompts/override-<step>-<workflow>-prompt.md`
- **Generated output**: `temp-<workflow>-<step>-prompt.md` in the workflow state directory

### Template Variables

Templates use `{{variable_name}}` syntax for substitution:

```markdown
# Working on {{jira_issue_key}}

You are working on Jira issue **{{jira_issue_key}}**.
```

Variables are populated from state, with dot notation converted to underscores:

- State key `jira.issue_key` → Template variable `{{jira_issue_key}}`
- State key `pull_request_id` → Template variable `{{pull_request_id}}`

### Override Templates

Users can create override templates to customize workflow prompts:

1. Copy the default template to an override file
2. Modify as needed
3. **Important**: Override templates cannot introduce new variables not present in the default

Example validation error:

```text
TemplateValidationError: Override template uses variables not in default: {'new_variable'}
```

### Creating Custom Workflows

To add a new workflow:

1. Create the default prompt template in `agentic_devtools/prompts/`
2. Add the workflow initiation function in `cli/workflows/commands.py`
3. Export the function in `cli/workflows/__init__.py`
4. Add the CLI entry point in `pyproject.toml`
5. Document the required state keys

## 7. Installation

```bash
# From the package directory (scripts/agentic_devtools)
pip install -e .

# Or with dev dependencies
pip install -e ".[dev]"
```

### Multi-Worktree State Isolation

When working with multiple git worktrees (e.g., one for feature development and another for the main branch),
the `agdt-ai-helpers` package uses **smart repo-local state detection** to keep state isolated per worktree.

**How it works:**

1. State files are stored in `.agdt/workflows/{identity}/{worktree_key}/` relative to the repository root
2. The `get_state_dir()` function resolves the path via `.agdt/runtime-bootstrap.json`
3. Directories are automatically created as needed
4. This ensures each worktree has its own isolated state, even with a single global pip installation

**State directory resolution priority:**

1. `AGENTIC_DEVTOOLS_STATE_DIR` environment variable (explicit override)
2. `.agdt/workflows/{identity}/{worktree_key}/` via bootstrap (auto-detected)
3. `.agdt/workflows/_unscoped/` fallback
4. `.agdt-temp/` in current working directory (fallback for non-repo contexts)

**New worktree setup:**
When creating a new worktree, `.agdt/workflows/` doesn't exist initially (it's gitignored). The helpers automatically create it on first use, so no manual setup is required.

**Tip:** Use the `agdt-initiate-work-on-jira-issue-workflow` command which includes worktree setup automation with VS Code integration.

## 8. Environment Variables

| Variable | Purpose |
|----------|---------||
| `AZURE_DEV_OPS_COPILOT_PAT` | PAT for Azure DevOps API calls |
| `JIRA_COPILOT_PAT` | PAT for Jira API calls |
| `JIRA_BASE_URL` | Override default Jira URL (default: `https://jira.swica.ch`) |
| `JIRA_SSL_VERIFY` | Set to "0" to disable SSL verification |
| `JIRA_CA_BUNDLE` | Path to custom CA bundle PEM file for Jira SSL |
| `REQUESTS_CA_BUNDLE` | Standard requests library CA bundle path (fallback) |
| `AGENTIC_DEVTOOLS_STATE_DIR` | Override default state directory (`.agdt/workflows/_unscoped`) |
| `AGDT_DRY_RUN` | Set to "1" for dry-run mode globally |
| `AGDT_PLAN_CONTEXT_BUDGET` | Plan-phase context budget in characters (default: `32000`). If set, oversized spec content is reduced deterministically before calling the LLM |

### SSL Certificate Handling

The Jira commands automatically handle SSL certificate verification for corporate internal CAs:

1. **Environment override**: Set `JIRA_SSL_VERIFY=0` to disable verification entirely
2. **Custom CA bundle**: Set `JIRA_CA_BUNDLE` to a path containing your CA certificates
3. **Repo-committed bundle**: The preferred CA bundle is committed at `scripts/jira_ca_bundle.pem` (contains the full certificate chain for jira.swica.ch)
4. **Auto-fetch fallback**: If the repo bundle doesn't exist, certificates are auto-fetched from the Jira server using `openssl s_client` and cached to `jira_ca_bundle.pem` in the state directory
5. **Last resort**: If auto-fetch fails, SSL verification is disabled with a warning

## 9. Adding New Commands

### Adding a new action command (background task pattern)

When adding a new command that performs side effects (API calls, git operations, file mutations):

1. **Add the sync function** in the appropriate module (e.g., `cli/azure_devops/commands.py`)
2. Read required state with `get_value()` or use existing helper functions like `parse_bool_from_state()`
3. Export the function in the module's `__init__.py`
4. **Create an async wrapper** that uses `run_in_background()` to spawn the sync command as a background task
5. **Add entry point** in `pyproject.toml`:

   ```toml
   [project.scripts]
   agdt-new-command = "agentic_devtools.cli.module.commands:new_command_async"
   ```

6. Reinstall: `pip install -e .`
7. **Document the command** in this file

### Adding new helper functions

1. Add pure utility functions (no state reading) to `cli/azure_devops/helpers.py`
2. Add functions that read state to `cli/azure_devops/commands.py`
3. Export in `__init__.py` if needed for external use

### Adding convenience state functions

Add typed functions in `state.py`:

```python
def get_new_field(required: bool = False) -> Optional[str]:
    """Get the new field from state."""
    return get_value("new_field", required=required)
```

## 10. Protected / Auto-Generated Files

> **⚠️ AI AGENTS: Never edit, stage, or commit the files listed here.**
> They are auto-generated at build time. Any local changes are noise and must be discarded.

### `agentic_devtools/_version.py`

Generated automatically by `hatch-vcs` / `setuptools-scm` from Git tags. Its header reads:
_"file generated by setuptools-scm — don't change, don't track in version control."_

The file is listed in `.gitignore` and is **not tracked by git**. **Do not** `git add`, edit, or
commit it. Because it is untracked, `.gitignore` prevents `git add .` from ever staging it —
this applies to all tools including `report_progress` and the Copilot coding agent's own git
operations.

> **ℹ️ Note:** `agdt-git-save-work` also explicitly unstages `agentic_devtools/_version.py`
> before creating a commit, so it is doubly protected. If you ever see it appearing in
> `git status`, do **not** stage or commit it. For test-specific guidance see `tests/README.md`.

- To bump the package version, create a new Git tag — see [RELEASING.md](../RELEASING.md).

### Identifying auto-generated files in the future

A file is auto-generated when it contains a comment such as:

```text
# file generated by <tool>
# don't change, don't track in version control
```

When you encounter such a comment in a file you are about to edit or commit, **stop** — the file
should not be touched manually.

### Excluding auto-generated files from source-scanning tools

Any script that iterates over `agentic_devtools/` source files (e.g., `scripts/scaffold_tests.py`)
must **explicitly exclude** `_version.py` by name, in addition to `__init__.py`. Even though
`_version.py` currently has no public functions, the exclusion makes the intent clear and prevents
the file from accidentally appearing in generated output if it ever gains a public symbol.

Pattern to follow:

```python
if p.name not in {"__init__.py", "_version.py"} and "__pycache__" not in p.parts
```

## 11. 1:1:1 Test Structure

All new tests **must** be placed under `tests/unit/` and follow the 1:1:1 policy.
For the full reference, see [tests/README.md](../tests/README.md).

### Policy Summary

- **One folder per source file** — the test path mirrors the source path.
- **One test file per symbol** — one function or class per test file.
- **Every directory must contain `__init__.py`**.

### Path Convention

```text
tests/unit/{module_path}/{source_file_name}/test_{symbol_name}.py
```

| Source symbol | Test file |
|---|---|
| `agentic_devtools/cli/git/core.py` → `get_current_branch()` | `tests/unit/cli/git/core/test_get_current_branch.py` |
| `agentic_devtools/state.py` → `get_value()` | `tests/unit/state/test_get_value.py` |
| `agentic_devtools/cli/workflows/worktree_setup.py` → `WorktreeSetupResult` | `tests/unit/cli/workflows/worktree_setup/test_worktreesetupresult.py` |

Symbol naming rules:

- **Functions**: exact snake\_case name (e.g., `get_current_branch` → `test_get_current_branch.py`).
- **Classes / dataclasses / enums**: class name lowercased **without** added underscores
  (e.g., `WorktreeSetupResult` → `test_worktreesetupresult.py`).

### Top-level source files (e.g., `state.py`, `background_tasks.py`)

Source files directly in `agentic_devtools/` (with no subdirectory) map to:

```text
tests/unit/{source_file_name}/test_{symbol_name}.py
```

For example:

- `agentic_devtools/state.py` → `tests/unit/state/test_get_workflow_state.py`
- `agentic_devtools/background_tasks.py` → `tests/unit/background_tasks/test_run_function_in_background.py`

The validator (`scripts/validate_test_structure.py`) requires a minimum of **2 path components**
under `tests/unit/`, so top-level source files are fully supported without any workaround.

> **⚠️ Do NOT create proxy/stub source files** (e.g., `agentic_devtools/root/state.py`) just to
> add an extra path component. This approach pollutes the package with files that serve no
> purpose beyond satisfying a validator that already handles the case natively.

### How to Add a New Test

1. Identify the source file, e.g. `agentic_devtools/cli/git/core.py`.
2. Create `tests/unit/cli/git/core/` (and parent dirs if missing), each with `__init__.py`.
3. Create `tests/unit/cli/git/core/test_<symbol>.py` for the function or class under test.
4. Run the validator: `python scripts/validate_test_structure.py`

See [tests/README.md](../tests/README.md) for complete step-by-step instructions and examples.

### CI Enforcement

`scripts/validate_test_structure.py` runs in CI and **fails the build** when it finds structural
issues in `tests/unit/` (incorrect source-file folder mapping or missing `__init__.py` files).
It does **not** verify that every symbol has a corresponding test file or that each
`test_<symbol>.py` maps to a real symbol — those parts of the 1:1:1 pattern are enforced via
convention and code review. Run it locally before pushing:

```bash
python scripts/validate_test_structure.py
```

## 12. Python Coding Patterns

### Import ordering (ruff/isort)

Ruff enforces isort-style import ordering (rule set `I`). All Python files must use this order:

1. **Standard library** imports
2. **Third-party** imports (e.g., `pytest`, `requests`)
3. **First-party** imports (`agentic_devtools.*` — the only first-party package; the legacy `agdt_ai_helpers` shim has been removed)

Within each group, `import X` lines come before `from X import Y` lines.

```python
# Correct
import os
import time
from unittest.mock import patch   # stdlib — same group as os/time

import pytest                     # third-party

from agentic_devtools.state import get_value  # first-party
```

```python
# Wrong — stdlib 'from unittest.mock import patch' placed after third-party 'import pytest'
import pytest
from unittest.mock import patch   # ← ruff I001 violation
```

To auto-fix: `ruff check --fix tests/` or `ruff check --fix --select I tests/`

### Dynamic script loading with `importlib`

When loading a script dynamically (e.g., loading a `scripts/*.py` file by path), always guard
against `None` returns from `spec_from_file_location()` before calling `module_from_spec()` and
`exec_module()`:

```python
import importlib.util

spec = importlib.util.spec_from_file_location("module_name", script_path)
if spec is None or spec.loader is None:
    raise RuntimeError(f"Could not load module from {script_path!s}")
module = importlib.util.module_from_spec(spec)
spec.loader.exec_module(module)
```

`spec_from_file_location()` returns `None` when the file cannot be found or the path is not
recognised as a loadable Python source. Without the guard, the very first call — `module_from_spec(spec)`
— raises an obscure `AttributeError: 'NoneType' object has no attribute ...` that hides the real
problem. The explicit `RuntimeError` surfaces the actual path that failed, making failures
trivially easy to diagnose.

## 13. Testing

**⚠️ AI AGENTS: ALWAYS use agdt-test commands, NEVER pytest directly!**

```bash
# Run tests (ALWAYS use these commands)
agdt-test          # Full suite with coverage (background, ~55s)
agdt-task-wait     # Wait for completion (REQUIRED!)

agdt-test-quick    # Fast run without coverage (background)
agdt-task-wait     # Wait for completion (REQUIRED!)

# For specific tests (with CLI arguments, runs synchronously)
agdt-test-pattern tests/test_state.py::TestSetValue

# Test a specific source file with 100% coverage requirement
agdt-test-file --source-file agentic_devtools/state.py  # Auto-saved for future runs
agdt-task-wait                                          # Wait for completion (REQUIRED!)
```

**WHY background tasks?** The test suite has 2000+ tests and takes ~55 seconds.
Running synchronously causes AI agents to think something went wrong during the
wait, leading to multiple restarts and wasted resources.

### TDD Workflow (Required for All Implementation Work)

**⚠️ AI AGENTS: Always follow the red-green-refactor TDD cycle. Write tests BEFORE
implementation code.**

For every new function, class, or behaviour change, follow this cycle:

#### Step 1 — RED: Write a failing test first

Create the test file following the 1:1:1 policy **before** touching source code:

```bash
# Create tests/unit/cli/git/core/test_new_function.py with expected behaviour
# Then confirm the test fails (RED):
agdt-test-pattern tests/unit/cli/git/core/test_new_function.py -v
# Expected output: FAILED
```

#### Step 2 — GREEN: Write the minimal implementation

Write only enough code to make the failing test pass:

```bash
# Edit agentic_devtools/cli/git/core.py with minimal implementation
# Then confirm tests pass (GREEN):
agdt-test-pattern tests/unit/cli/git/core/test_new_function.py -v
# Expected output: PASSED
```

#### Step 3 — REFACTOR: Improve without breaking tests

Tidy the code while keeping tests green. Use `agdt-test-pattern` pointed at the
1:1:1 test folder for the source file — **not** `agdt-test-file`, which only works
with legacy flat test files and will fail for any file under `tests/unit/`:

```bash
# Refactor and re-run focused tests:
agdt-test-pattern tests/unit/cli/git/core/ -v
```

#### Step 4 — Full suite check

After all checklist items are complete, run the full test suite:

```bash
agdt-test
agdt-task-wait
```

#### Why TDD?

- Ensures tests reflect **intended** behaviour, not implementation accidents.
- Forces minimal code — no speculative features that lack test coverage.
- Aligns with the existing 100% coverage requirement already enforced in CI.

## 14. Pre-commit Hooks

The repository has pre-commit hooks for linting Python files in `scripts/`. To enable:

```bash
git config core.hooksPath .githooks
```

The hooks run automatically on `git commit` and check:

- **ruff check**: Lints for pycodestyle errors (E), Pyflakes (F - unused imports/variables), warnings (W), import sorting (I), and pyupgrade (UP)
- **ruff format**: Auto-formats code
- **cspell**: Checks spelling against the dictionary in `cspell.json`

To disable hooks:

```bash
git config --unset core.hooksPath
```

To run checks manually:

```bash
# Ruff lint (with auto-fix)
ruff check --fix --config scripts/agentic_devtools/pyproject.toml scripts/agentic_devtools/

# Ruff format
ruff format --config scripts/agentic_devtools/pyproject.toml scripts/agentic_devtools/

# cspell (use global install, not npx)
cspell lint "scripts/**/*.py"
```

### cspell Dictionary Setup

The `cspell.json` file is the single source of truth for spelling. The VS Code workspace imports it via `cSpell.import`.

**Required global installs** (one-time setup, requires disconnecting from VPN):

```bash
npm install -g cspell @cspell/dict-de-de @cspell/dict-python @cspell/dict-dotnet @cspell/dict-companies @cspell/dict-fullstack @cspell/dict-typescript
```

To add new words, edit `cspell.json` directly (keep alphabetically sorted). Multiple language dictionaries are enabled via imports in `cspell.json`.

## 15. Commit Message Convention

Every commit **must** follow [Conventional Commits v1.0.0](https://www.conventionalcommits.org)
with a mandatory GitHub issue link as the scope. See [COMMIT_CONVENTION.md](../COMMIT_CONVENTION.md)
for the full specification.

### Quick reference

```text
type([#NNN](https://github.com/ayaiayorg/agentic-devtools/issues/NNN)): summary

body (optional bullet points)

[#NNN](https://github.com/ayaiayorg/agentic-devtools/issues/NNN)
```

**Rules for AI agents:**

- The scope is **never** optional — always include a GitHub issue markdown link.
- The footer **must** repeat the same issue link(s) as the scope.
- Breaking changes: use `!` after the scope closing `)` **and** prefix the footer with `BREAKING CHANGE:`.
- Supported types: `feat`, `fix`, `docs`, `style`, `refactor`, `perf`, `test`, `build`, `ci`, `chore`, `revert`.
- Parent issue comes **first** in parent/child links (scope: `parent/child`, footer: `parent / child`).
- Multiple unrelated issues: comma-separated, ascending order by number.
- **Do NOT** use old Jira-style scopes like `feat(PROJECT-1234):` — the scope must always be a GitHub issue markdown link `([#NNN](...))`.
- Branch names follow the `type/ISSUE-KEY/description` convention (e.g. `feature/PROJECT-1234/add-webhook`) — this is separate from the commit scope.

### Examples

Single issue:

```text
feat([#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): add webhook support

- Implemented webhook handler
- Added unit tests

[#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)
```

Parent + child issue:

```text
feat([#10](https://github.com/ayaiayorg/agentic-devtools/issues/10)/[#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): implement sub-feature

- Added endpoint
- Wired up Jira notification

[#10](https://github.com/ayaiayorg/agentic-devtools/issues/10) / [#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)
```

## 16. Common Workflows

> **Note:** All action commands (those that mutate state or make API calls) spawn background tasks.
> These return immediately. Use `agdt-task-status` or `agdt-task-wait` to monitor.

### Initial Git Commit & Publish

```bash
# Option A: With CLI parameter (explicit)
agdt-git-save-work --commit-message "feat([#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): implement feature

- Added new component
- Updated tests

[#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)"
# Returns task ID immediately - use agdt-task-wait to block until complete

# Option B: Parameterless (uses current state)
# Current commit_message: run `agdt-get commit_message` to check
agdt-git-save-work
```

### Amend Commit (Single Commit Policy - Automatic Detection)

`agdt-git-save-work` now automatically detects when to amend instead of creating a new commit:

- If current branch has commits ahead of main AND the last commit contains the same issue key → amend
- Otherwise → new commit

```bash
# Option A: With CLI parameter (explicit)
agdt-git-save-work --commit-message "feat([#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): implement feature

- Added new component
- Updated tests
- Addressed PR feedback

[#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)"
# Automatically amends if already pushed a commit for this issue

# Option B: Parameterless (uses current state)
# Current commit_message: run `agdt-get commit_message` to check
agdt-git-save-work
```

### Create a Pull Request

```bash
agdt-set source_branch feature/PROJECT-1234/my-changes
agdt-set title "feat([#42](https://github.com/ayaiayorg/agentic-devtools/issues/42)): Add new feature"
agdt-set description "This PR implements the new feature."
agdt-create-pull-request
```

### Create a Draft PR (default)

```bash
agdt-set source_branch feature/my-branch
agdt-set title "My PR Title"
agdt-create-pull-request
# Note: PRs are created as drafts by default
```

### Create a Non-Draft PR

```bash
agdt-set source_branch feature/my-branch
agdt-set title "My PR Title"
agdt-set draft false
agdt-create-pull-request
```

### Reply to PR Thread

```bash
agdt-set pull_request_id 23046
agdt-set thread_id 139474
agdt-set content "Thanks for the feedback!

I've addressed your concerns."
agdt-reply-to-pull-request-thread
```

### Reply and Resolve Thread

```bash
agdt-set pull_request_id 23046
agdt-set thread_id 139474
agdt-set resolve_thread true
agdt-set content "Fixed, resolving thread."
agdt-reply-to-pull-request-thread
```

### Add a PR Comment

```bash
agdt-set pull_request_id 23046
agdt-set content "Here's a general comment on this PR."
agdt-add-pull-request-comment
```

### Add a PR Comment with Approval Sentinel

```bash
agdt-set pull_request_id 23046
agdt-set content "LGTM! All acceptance criteria met."
agdt-set is_pr_approval true
agdt-add-pull-request-comment
```

### Approve a Pull Request (Convenience Command)

```bash
agdt-set pull_request_id 23046
agdt-set content "LGTM! Great work on this feature."
agdt-approve-pull-request
# Note: This automatically adds the approval sentinel banner
```

### Resolve a Thread

```bash
agdt-set pull_request_id 23046
agdt-set thread_id 139474
agdt-resolve-thread
```

### Get All PR Threads (Sync - Immediate Output)

```bash
agdt-set pull_request_id 23046
agdt-get-pull-request-threads
```

### Dry Run Mode

```bash
agdt-set dry_run true
agdt-git-save-work  # Previews without executing git commands
agdt-reply-to-pull-request-thread  # Previews without API calls
```

### Pull Request Review Workflow

The end-to-end automated PR review is initiated with a **single command**:

```bash
# Start with a PR ID (interactive mode — VS Code terminal)
agdt-initiate-pull-request-review-workflow --pull-request-id 12345

# Start with a Jira issue key (looks up the PR automatically)
agdt-initiate-pull-request-review-workflow --issue-key PROJECT-1234

# Non-interactive / pipeline mode
agdt-initiate-pull-request-review-workflow --pull-request-id 12345 --interactive false
```

**Automated flow:**

1. Resolves both the PR ID and Jira issue key (cross-lookup when only one is provided).
2. Fetches the PR source branch from Azure DevOps.
3. Validates the current worktree/branch context via pre-flight checks.
4. If the context is wrong, **automatically creates a dedicated worktree**, attempts to open VS Code (when available), then re-runs the command inside the new worktree.
5. Fetches full PR details (diff, threads, iterations) and Jira issue details.
6. Generates per-file review prompts in `pull-request-review/<commit_hash_short>/` under the state directory.

    > **⚠️ Migration note (upgrading from pre-refactor versions):**
    > The artifact directory layout changed from `pull-request-review/prompts/<pr_id>/` to
    > `pull-request-review/<commit_hash_short>/` in this release.
    > `_get_queue_path` transparently falls back to the legacy path when the new path's
    > `queue.json` is absent but the old one exists, so **in-progress reviews continue to
    > work after upgrade without any manual migration**.  Once a new review session is
    > started (via `agdt-review-pull-request`), artifacts for that PR will be written to
    > the new path.  Artifacts from the old path can be safely deleted after all active
    > reviews complete.

7. **When auto-setup ran (new worktree was created):** starts a `gh copilot` CLI session
   (interactive or background depending on `--interactive`). When already in the correct
   worktree context, the rendered initiate prompt is printed to the console for the agent
   to use manually.

#### `--interactive` Flag

| Value | Behavior (when a Copilot session is started) |
|-------|----------------------------------------------|
| `true` (default) | Starts `gh copilot suggest` with an attached terminal — the reviewer interacts with it directly in VS Code. |
| `false` | Starts `gh copilot suggest` as a detached background process, capturing output to `.agdt/workflows/…/background-tasks/logs/`. Use for Azure DevOps pipelines or other headless environments. |

If `gh copilot` is not installed, a warning is printed and the prompt file path is shown so the review can be started manually.

#### Generated Review Artifacts

| File | Purpose |
|------|---------|
| `review-state.json` | Hierarchical review state: PR, folder, and file thread IDs, statuses, and suggestions |
| `queue.json` | Review queue manifest (pending/completed files) |
| `pull-request-files.json` | Snapshot of all PR files |
| `pull-request-threads.json` | Snapshot of existing comment threads |
| `pull-request-jira-issue.json` | Copy of linked Jira issue |
| `file-<hash>.md` | Individual file review prompt with diff and threads |

#### File Review Commands

After a review session is active, use these commands for each file:

```bash
# Approve a file (no issues found)
agdt-set pull_request_id 23523
agdt-set file_review.file_path "/path/to/file.ts"
agdt-set file_review.summary "LGTM - code follows conventions"
agdt-approve-file

# Request changes (with suggestions)
agdt-set file_review.summary "Error handling issues found."
agdt-set file_review.suggestions '[{"line": 42, "severity": "high", "content": "Consider using a more descriptive variable name"}]'
agdt-request-changes

# Request changes with code suggestion
agdt-set file_review.summary "Naming issue found."
agdt-set file_review.suggestions '[{"line": 42, "severity": "medium", "content": "Use a more descriptive variable name", "replacement_code": "const descriptiveVariableName = value;"}]'
agdt-request-changes-with-suggestion
```

#### Hierarchical Review Thread Architecture

`agdt-review-pull-request` scaffolds a three-level comment hierarchy in Azure DevOps **before**
reviewing any files:

1. **File threads** — one anchored comment per file (no line context); updated via PATCH
   as each file is approved or has changes requested
2. **Folder threads** — one PR-level thread per top-level folder grouping, with links to
   each file thread; status cascades from file statuses
3. **Overall PR summary thread** — a single top-level thread linking all folder threads;
   status cascades from folder statuses

All threads are created during scaffolding and updated in-place (PATCH) as files are
reviewed.

#### Review State File (`review-state.json`)

Location: `<state_dir>/reviews/review-state.json` (where `<state_dir>` is `.agdt/workflows/{identity}/{worktree_key}`)

This file tracks all thread IDs, statuses, and suggestions for the entire review session:

```json
{
  "prId": 12345,
  "repoId": "<guid>",
  "repoName": "my-repo",
  "project": "MyProject",
  "organization": "myorg",
  "latestIterationId": 1,
  "scaffoldedUtc": "2024-12-19T15:50:26+00:00",
  "overallSummary": { "threadId": 1, "commentId": 1, "status": "in-progress" },
  "folders": {
    "src/app": { "threadId": 2, "commentId": 1, "status": "in-progress", "files": ["/src/app/component.ts"] }
  },
  "files": {
    "/src/app/component.ts": {
      "threadId": 3,
      "commentId": 1,
      "folder": "src/app",
      "fileName": "component.ts",
      "status": "approved",
      "summary": "Clean implementation, no issues found.",
      "suggestions": [],
      "previousSuggestions": null
    }
  }
}
```

#### Review Status State Machine

Each file, folder, and the overall PR follow this status progression:

```text
unreviewed → in-progress → approved
                        ↘ needs-work
```

- `unreviewed` — not yet started (initial state)
- `in-progress` — review started but not all files in scope are complete
- `approved` — all files approved (no blocking issues)
- `needs-work` — at least one file has changes requested

#### Status Derivation Rules

| Level | Rule |
|-------|------|
| **File** | Set directly by `agdt-approve-file` (→ `approved`) or `agdt-request-changes` (→ `needs-work`) |
| **Folder** | All files unreviewed → `unreviewed`; ≥1 started, not all done → `in-progress`; all done, all approved → `approved`; all done, any needs-work → `needs-work` |
| **Overall PR** | Same rules as folder, applied to folder statuses |

#### Suggestion Severity Levels

| Severity | Meaning |
|----------|---------|
| `high` | Blocking — must be addressed before the PR can be approved |
| `medium` | Should be addressed but not strictly blocking |
| `low` | Nice-to-have improvement; can be deferred |

#### Out-of-Scope Suggestions

When a suggestion does not map to a specific line in the diff (e.g., an architectural
concern or a comment on a non-changed line), set `"out_of_scope": true` in the suggestion
entry. The `out_of_scope` flag is persisted on the suggestion entry for classification, but
suggestions are still posted as line-anchored file threads (not PR-level comments).

#### Re-Review Flow

When an author addresses feedback and requests a re-review:

1. File status is reset from the terminal state (`approved`/`needs-work`) to `in-progress`
2. Existing `suggestions` are rotated to `previousSuggestions` as an audit trail
3. New suggestions can be added from scratch for the fresh review

The rotation fires **once** per re-review cycle (when `previousSuggestions is None`).
Once rotated — even if the original suggestions list was empty — `previousSuggestions`
is set to `[]` (not `null`), so retries are safe and will not re-trigger rotation.

#### Pipeline Usage

For use in Azure DevOps pipelines (headless, no interactive terminal):

```yaml
# azure-pipelines.yml example
- script: agdt-initiate-pull-request-review-workflow --pull-request-id $(System.PullRequest.PullRequestId) --interactive false
  displayName: 'Run automated PR review'
  env:
    AZURE_DEV_OPS_COPILOT_PAT: $(AzureDevOpsCopilotPat)
    JIRA_COPILOT_PAT: $(JiraCopilotPat)
```

When running in pipeline mode (`--interactive false`):

- `gh copilot` output is captured to `.agdt/workflows/…/background-tasks/logs/copilot_session_*.log`.
- The Copilot process runs as a direct child process (via `subprocess.Popen`), not as an
  agdt background task, so there is no background task ID and `agdt-task-wait` is not
  applicable. Monitor completion using the `copilot.pid` state key and/or by tailing the
  Copilot session log file.
- The `worktree_setup.auto_execute_exit_code` state key records the exit code of the
  setup/auto-execute command, not the Copilot session itself.

#### Copilot / VS Code Graceful Degradation

When an interactive Copilot session cannot be started, the workflow falls back to a
non-interactive mode:

- If `gh copilot` is not available on the machine, a warning is printed to stderr.
- If the VS Code `code` CLI is not available, or there is no attached TTY (for example,
  in CI pipelines), interactive mode is automatically disabled and `copilot.mode` is set
  to `"non-interactive"`.
- In all of these cases, the rendered prompt is written to
  `copilot-session-<session_id>-prompt.md` in the state directory, and the session metadata is still
  persisted to state (`copilot.*` keys).
- The reviewer can open the prompt file in VS Code (or any editor) and start a manual
  Copilot session if desired.

#### Copilot CLI Session Management

State keys written to `agdt-state.json` after a session is started:

| Key | Type | Description |
|-----|------|-------------|
| `copilot.session_id` | string | UUID4 hex identifying the session |
| `copilot.mode` | string | `"interactive"` or `"non-interactive"` |
| `copilot.prompt_file` | string | Absolute path to the temporary prompt file |
| `copilot.start_time` | string | ISO-8601 UTC timestamp when the session was started |
| `copilot.pid` | `integer \| ""` | PID of background process (empty for interactive sessions) |

Additional `worktree_setup` keys written during automated environment setup:

| Key | Type | Description |
|-----|------|-------------|
| `worktree_setup.auto_execute_exit_code` | string | Exit code of the auto-executed setup command |

#### Target Repository Configuration (`.github/agdt-config.json`)

Target repositories can place a `.github/agdt-config.json` file in their root to customize the review workflow. The file is **optional** — if absent, the review proceeds with defaults.

**Schema:**

```json
{
  "review": {
    "focus-areas-file": ".github/review-focus-areas.md"
  }
}
```

| Field | Type | Description |
|-------|------|-------------|
| `review.focus-areas-file` | string | Repo-root-relative path to a markdown file listing review focus areas. |

**`.github/review-focus-areas.md` format:**

Free-form markdown injected into the review prompt to guide the Copilot reviewer. Example:

```markdown
## Review Focus Areas

- Ensure all public APIs have JSDoc/docstring documentation.
- Validate that new database migrations are backward-compatible.
- Check that error messages are user-friendly and don't leak internals.
```

Both files are optional and safe to omit; the review will still run without repo-specific guidance.

### Get Jira Issue Details

```bash
agdt-set jira.issue_key PROJECT-1234
agdt-get-jira-issue
```

This fetches the issue and:

- Prints formatted details (key, summary, type, labels, description, comments)
- Saves full JSON response to `temp-get-issue-details-response.json` in the state directory
- Stores issue in state as `jira.last_issue`

### Add Comment to Jira Issue

```bash
agdt-set jira.issue_key PROJECT-1234
agdt-set jira.comment "h4. Progress Update

*Completed:*
* Task 1
* Task 2

*Next Steps:*
* Task 3"
agdt-add-jira-comment
```

After posting, the command automatically refreshes issue details.

### Create Jira Epic

```bash
agdt-set jira.project_key PROJECT
agdt-set jira.summary "My Epic Title"
agdt-set jira.epic_name "My Epic Name"
agdt-set jira.role "developer"
agdt-set jira.desired_outcome "a new feature"
agdt-set jira.benefit "improved productivity"
agdt-create-epic
```

### Create Jira Issue

```bash
agdt-set jira.project_key PROJECT
agdt-set jira.summary "Bug: Something is broken"
agdt-set jira.description "Detailed description here"
agdt-create-issue
```

Or use the user story format:

```bash
agdt-set jira.project_key PROJECT
agdt-set jira.summary "Feature request"
agdt-set jira.role "user"
agdt-set jira.desired_outcome "new capability"
agdt-set jira.benefit "better experience"
agdt-create-issue
```

### Create Subtask

```bash
agdt-set jira.parent_key PROJECT-1234
agdt-set jira.summary "Subtask title"
agdt-set jira.description "Subtask details"
agdt-create-subtask
```

### Jira Dry Run Mode

```bash
agdt-set jira.dry_run true
agdt-add-jira-comment  # Previews without posting
```

## 17. Output Files

| File | Command | Content |
|------|---------|---------|
| `.agdt/workflows/…/state.json` | All commands | Persistent state storage |
| `.agdt/workflows/…/temp-get-issue-details-response.json` | `agdt-get-jira-issue` | Full Jira API response |
| `.agdt/workflows/…/temp-get-pull-request-details-response.json` | `agdt-get-pull-request-details` | Full PR details payload |
| `.agdt/workflows/…/pull-request-review/<commit_hash_short>/` | `agdt-review-pull-request` | Review prompts directory |
| `.agdt/workflows/…/reviews/review-state.json` | `agdt-review-pull-request` | Hierarchical review state (thread IDs, statuses, suggestions) |
| `.agdt/workflows/…/temp-<workflow>-<step>-prompt.md` | Workflow initiation commands | Rendered workflow prompts |

### Commit Hash Source of Truth

The PR commit hash is stored in multiple locations, each serving a distinct purpose.

| Location | Field | Format | Purpose |
|----------|-------|--------|---------|
| `review-state.json` | `commitHash` | Full 40-char SHA | **Canonical** source of truth for the reviewed commit, set from `lastMergeSourceCommit.commitId` during scaffolding |
| `state.json` | `review.commit_hash_short` | First 12 chars | Derived from the canonical hash; used as the artifact directory name under `pull-request-review/` |
| `review-state.json` | `sessions[].commitHash` | Full 40-char SHA | Records which commit each individual review session targeted (may differ across sessions after new pushes) |
| Artifact directory | `pull-request-review/<hash>/` | First 12 chars | On-disk directory scoping review prompts and queue files, derived from the canonical hash |

`review-state.json` → `commitHash` is the **canonical** full commit hash for the PR under review.
`state.json` → `review.commit_hash_short` is **derived** from it (first 12 characters) and used for artifact directory resolution.
Legacy 8-character directory names may still be recognized as a backward-compatibility fallback.
Per-session `commitHash` records which specific commit each review session targeted, which may differ from the top-level `commitHash` when the PR is re-reviewed after new pushes.

### Background Task Storage Structure

Background tasks use a separate storage structure in `.agdt/workflows/…/background-tasks/`:

```text
.agdt/workflows/{identity}/{worktree_key}/
├── state.json                         # Main state file (contains background.recentTasks)
└── background-tasks/
    ├── all-background-tasks.json      # Complete history of all tasks (never pruned)
    └── logs/
        └── <command>_<timestamp>.log  # Task output logs
```

**State Structure:**

The `agdt-state.json` file contains recent tasks under `background.recentTasks`:

```json
{
  "background": {
    "recentTasks": [
      {
        "id": "task-abc123",
        "command": "agdt-git-save-work",
        "status": "completed",
        "start_time": "2024-12-19T15:50:26Z",
        "end_time": "2024-12-19T15:50:28Z",
        "exit_code": 0,
        "log_file": "/path/to/logs/agdt_git_commit_20241219_155026.log"
      }
    ],
    "task_id": "task-abc123"
  }
}
```

**Sorting Rules:**

- Unfinished tasks appear first, sorted by start time (earliest first)
- Finished tasks appear after, sorted by end time (earliest first)

**Auto-Pruning:**

- Recent tasks are automatically pruned when not running and finished more than 5 minutes ago
- The `all-background-tasks.json` file keeps the complete history without pruning

## 18. Instruction Maintenance

Update this file when:

- Adding new CLI commands
- Changing state file structure
- Modifying the auto-approval pattern
- Adding new integrations
- Adding new workflow commands or prompt templates
- Discovering new anti-patterns that AI agents should be warned about
