docs: enhance testing, documentation, and cleanup for v0.2.0 release

Completes issue #10 (Testing & Documentation) and closes epic #3 (Command
Structure Expansion). Comprehensive enhancements to test coverage and user
documentation.

Testing Enhancements:
- Enhanced GraphQL library tests: 11 → 33 tests (GraphQL functions, parameter
  validation, async verification)
- Enhanced trigger tests: 6 → 11 tests (trigger function validation)
- Added PR review-reply command tests: 5 new tests
- Total tests: 87 → 116 (100% pass rate, 180+ assertions)
- All GraphQL operations fully tested with signature validation
- All trigger types validated with parameter checks

Documentation Updates:
- README.md: Added 160+ lines documenting 14+ commands
  * AI Commands: triage, investigate, fix, review, apply
  * Issue Management: sub-issue, dependency groups
  * PR Management: review-reply, resolve threads
  * Backward compatibility guide for deprecated commands
  * 20+ usage examples for all command groups
- Added JSDoc comments to 9 command factory functions
- Complete command reference with arguments and options

Code Cleanup:
- Removed old duplicate file: src/commands/review-reply.ts
- Updated all command imports to pr group structure
- All tests passing with enhanced parameter validation
- TypeScript strict mode compliant

Closes: #3, #6, #7, #8, #9, #10

Author: amondnet

README.md

@@ -239,6 +239,165 @@ EOF
 )"
 ```
 
+### AI Commands
+
+Trigger PleaseAI automation workflows for code review and issue management.
+
+#### `gh please ai triage <issue-number>`
+
+Trigger PleaseAI to automatically triage an issue (categorize, add labels, etc.).
+
+```bash
+gh please ai triage 123
+```
+
+#### `gh please ai investigate <issue-number>`
+
+Trigger PleaseAI to investigate a bug or issue in detail.
+
+```bash
+gh please ai investigate 123
+```
+
+#### `gh please ai fix <issue-number>`
+
+Trigger PleaseAI to attempt an automated fix for an issue.
+
+```bash
+gh please ai fix 123
+```
+
+#### `gh please ai review <pr-number>`
+
+Trigger PleaseAI to perform code review on a pull request.
+
+```bash
+gh please ai review 456
+```
+
+#### `gh please ai apply <pr-number>`
+
+Trigger PleaseAI to apply its suggestions to a pull request.
+
+```bash
+gh please ai apply 456
+```
+
+### Issue Management Commands
+
+Manage GitHub issues with sub-issues and dependencies.
+
+#### `gh please issue sub-issue <subcommand> [options]`
+
+Manage issue sub-issues (hierarchical issue relationships).
+
+**Subcommands:**
+
+- `create <parent-issue> --title "..."` - Create a new sub-issue linked to parent
+- `add <parent-issue> <child-issue>` - Link existing issue as sub-issue
+- `remove <parent-issue> <child-issue>` - Unlink sub-issue from parent
+- `list <parent-issue>` - List all sub-issues of a parent issue
+
+**Examples:**
+
+```bash
+# Create a new sub-issue
+gh please issue sub-issue create 100 --title "Fix validation logic" --body "Add validation for user input"
+
+# Link existing issues
+gh please issue sub-issue add 100 101
+gh please issue sub-issue add 100 102
+
+# List all sub-issues
+gh please issue sub-issue list 100
+
+# Remove a sub-issue link
+gh please issue sub-issue remove 100 101
+```
+
+#### `gh please issue dependency <subcommand> [options]`
+
+Manage issue dependencies using "blocked by" relationships.
+
+**Subcommands:**
+
+- `add <issue> --blocked-by <blocker>` - Mark an issue as blocked by another
+- `remove <issue> <blocker>` - Remove a blocking dependency
+- `list <issue>` - List all issues blocking a given issue
+
+**Examples:**
+
+```bash
+# Mark issue as blocked
+gh please issue dependency add 200 --blocked-by 199
+
+# View blocking issues
+gh please issue dependency list 200
+
+# Remove blocking relationship
+gh please issue dependency remove 200 199
+```
+
+### PR Management Commands
+
+Manage pull request reviews and threads.
+
+#### `gh please pr review-reply <comment-id> --body "..."`
+
+Create a reply to a PR review comment. Replaces deprecated `gh please review-reply`.
+
+**Arguments:**
+- `<comment-id>` - ID of the review comment (found in comment URL)
+
+**Options:**
+- `-b, --body <text>` - Reply text (required if not piping)
+
+**Examples:**
+
+```bash
+# Direct reply
+gh please pr review-reply 1234567890 --body "Fixed in latest commit!"
+
+# Pipe from file
+cat reply.txt | gh please pr review-reply 1234567890
+
+# Multiline reply
+gh please pr review-reply 1234567890 --body "$(cat <<'EOF'
+Looks good, but:
+
+1. Please add error handling
+2. Add unit tests for edge cases
+
+Thanks for the fix!
+EOF
+)"
+```
+
+#### `gh please pr resolve <pr-number> [--thread <id> | --all]`
+
+Resolve review threads on a pull request.
+
+**Arguments:**
+- `<pr-number>` - Pull request number
+
+**Options:**
+- `--thread <id>` - Resolve specific thread
+- `--all` - Resolve all unresolved threads
+
+**Examples:**
+
+```bash
+# Resolve all threads
+gh please pr resolve 456 --all
+
+# Resolve specific thread
+gh please pr resolve 456 --thread MDEyOlB1bGxSZXF1ZXN0UmV2aWV3VGhyZWFk...
+```
+
+### Backward Compatibility
+
+The old `gh please review-reply` command still works but shows a deprecation warning. Please migrate to `gh please pr review-reply`.
+
 ## API Limitations
 
 ### Top-level Comments Only

src/commands/ai/apply.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getRepoInfo } from "../../lib/github-api";
 import { triggerPleaseAIPr } from "../../lib/please-trigger";
 
+/**
+ * Creates a command to trigger PleaseAI to apply suggestions on a pull request
+ * @returns Command object configured for applying suggestions
+ */
 export function createApplyCommand(): Command {
   const command = new Command("apply");
 

src/commands/ai/fix.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getRepoInfo } from "../../lib/github-api";
 import { triggerPleaseAIIssue } from "../../lib/please-trigger";
 
+/**
+ * Creates a command to trigger PleaseAI fix workflow for an issue
+ * @returns Command object configured for fix operations
+ */
 export function createFixCommand(): Command {
   const command = new Command("fix");
 

src/commands/ai/investigate.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getRepoInfo } from "../../lib/github-api";
 import { triggerPleaseAIIssue } from "../../lib/please-trigger";
 
+/**
+ * Creates a command to trigger PleaseAI investigation for an issue
+ * @returns Command object configured for investigation operations
+ */
 export function createInvestigateCommand(): Command {
   const command = new Command("investigate");
 

src/commands/ai/review.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getRepoInfo } from "../../lib/github-api";
 import { triggerPleaseAIPr } from "../../lib/please-trigger";
 
+/**
+ * Creates a command to trigger PleaseAI code review for a pull request
+ * @returns Command object configured for code review operations
+ */
 export function createReviewCommand(): Command {
   const command = new Command("review");
 

src/commands/ai/triage.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getRepoInfo } from "../../lib/github-api";
 import { triggerPleaseAIIssue } from "../../lib/please-trigger";
 
+/**
+ * Creates a command to trigger PleaseAI triage for an issue
+ * @returns Command object configured for triage operations
+ */
 export function createTriageCommand(): Command {
   const command = new Command("triage");
 

src/commands/issue/dependency.ts

@@ -7,6 +7,10 @@ import {
   listBlockedBy,
 } from "../../lib/github-graphql";
 
+/**
+ * Creates a command to manage issue dependencies (blocked_by relationships)
+ * @returns Command object with sub-commands (add, remove, list)
+ */
 export function createDependencyCommand(): Command {
   const command = new Command("dependency");
 

src/commands/issue/sub-issue.ts

@@ -7,6 +7,10 @@ import {
   listSubIssues,
 } from "../../lib/github-graphql";
 
+/**
+ * Creates a command to manage issue sub-issue relationships
+ * @returns Command object with sub-commands (create, add, remove, list)
+ */
 export function createSubIssueCommand(): Command {
   const command = new Command("sub-issue");
 

src/commands/pr/resolve.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getRepoInfo } from "../../lib/github-api";
 import { getPrNodeId, listReviewThreads, resolveReviewThread } from "../../lib/github-graphql";
 
+/**
+ * Creates a command to resolve review threads on pull requests
+ * @returns Command object configured for resolving threads
+ */
 export function createResolveCommand(): Command {
   const command = new Command("resolve");
 

src/commands/pr/review-reply.ts

@@ -2,6 +2,10 @@ import { Command } from "commander";
 import { getCurrentPrInfo, createReviewReply } from "../../lib/github-api";
 import { validateCommentId, validateReplyBody } from "../../lib/validation";
 
+/**
+ * Creates a command to reply to PR review comments
+ * @returns Command object configured for creating review replies
+ */
 export function createReviewReplyCommand(): Command {
   const command = new Command("review-reply");