docs: add API Reference, environment variables, and command help (DOC-003, DOC-005, DOC-008)

README.md:
- Add comprehensive API Reference section with services, models, operations
- Document all environment variables with descriptions and defaults
- Add Hook Configuration section with all hook-specific variables

CLAUDE.md:
- Add Code Intelligence (LSP) section with hook documentation
- Add Navigation & Understanding guidance
- Add Verification Workflow and Pre-Edit Checklist

commands/*.md:
- Add consistent --help support with man-page style output
- Add help_check sections for early help detection

Addresses: DOC-003 (API Reference), DOC-005 (environment variables), DOC-008 (Related Commands)

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: zircote

CLAUDE.md

@@ -187,3 +187,41 @@ def capture_service(tmp_path, monkeypatch):
 | `HOOK_DEBUG` | Enable debug logging to stderr | `false` |
 | `HOOK_SESSION_START_INCLUDE_GUIDANCE` | Include response guidance templates | `true` |
 | `HOOK_SESSION_START_GUIDANCE_DETAIL` | Guidance level: minimal/standard/detailed | `standard` |
+
+## Code Intelligence (LSP)
+
+LSP hooks are configured in `.claude/hooks.json` for immediate feedback on Python edits.
+
+### Installed Hooks
+
+| Hook | Trigger | Action |
+|------|---------|--------|
+| `format-on-edit` | PostToolUse (Write/Edit) | Runs `ruff format` on changed files |
+| `lint-check-on-edit` | PostToolUse (Write/Edit) | Runs `ruff check` on changed files |
+| `typecheck-on-edit` | PostToolUse (Write/Edit) | Runs `mypy` on changed files |
+| `pre-commit-quality-gate` | PreToolUse (git commit) | Runs full `make quality` before commit |
+
+### Navigation & Understanding
+
+- Use LSP `goToDefinition` before modifying unfamiliar functions, classes, or modules
+- Use LSP `findReferences` before refactoring any symbol to understand full impact
+- Use LSP `documentSymbol` to get file structure overview before major edits
+- Prefer LSP navigation over grep—it resolves through imports and re-exports
+
+### Verification Workflow
+
+1. After each edit, check hook output for lint/type errors
+2. Fix errors immediately before proceeding
+3. Run `make quality` before committing
+
+### Pre-Edit Checklist
+
+- [ ] Navigate to definition to understand implementation
+- [ ] Find all references to assess change impact
+- [ ] Review type annotations via hover before modifying function signatures
+
+### Error Handling
+
+- If hooks report errors, fix them before proceeding to the next task
+- Type errors are blocking in this project (mypy strict mode)
+- Use hook output to guide fixes, not guesswork

README.md

@@ -57,6 +57,63 @@ recall = get_recall_service()
 memories = recall.search("database choice", namespace="decisions", limit=5)
 ```
 
+## API Reference
+
+### Core Services
+
+The library exposes three primary service interfaces via factory functions:
+
+| Service | Factory Function | Description |
+|---------|-----------------|-------------|
+| `CaptureService` | `get_capture_service()` | Capture memories with validation, git notes storage, and indexing |
+| `RecallService` | `get_recall_service()` | Search memories using semantic (vector) or text-based queries |
+| `SyncService` | `get_sync_service()` | Synchronize the SQLite index with git notes, verify consistency |
+
+### Key Models
+
+All models are immutable dataclasses (`frozen=True`) for thread-safety:
+
+| Model | Description |
+|-------|-------------|
+| `Memory` | Core entity representing a captured memory (id, namespace, summary, content, timestamp, tags) |
+| `MemoryResult` | Memory with similarity distance score from vector search |
+| `CaptureResult` | Result of capture operation (success, memory, indexed, warning) |
+| `IndexStats` | Statistics about the memory index (total, by_namespace, by_spec, last_sync) |
+| `HydrationLevel` | Enum for progressive loading: `SUMMARY`, `FULL`, `FILES` |
+
+### Common Operations
+
+```python
+from git_notes_memory import get_capture_service, get_recall_service, get_sync_service
+
+# Capture with tags
+capture = get_capture_service()
+result = capture.capture(
+    namespace="learnings",
+    summary="pytest fixtures can be module-scoped",
+    content="Use @pytest.fixture(scope='module') for expensive setup",
+    tags=["pytest", "testing"],
+)
+
+# Semantic search with filters
+recall = get_recall_service()
+results = recall.search(
+    query="database configuration",
+    k=10,                    # max results
+    namespace="decisions",   # filter by namespace
+    min_similarity=0.5,      # minimum relevance threshold
+)
+
+# Sync and verify index
+sync = get_sync_service()
+sync.reindex(full=True)  # full reindex from git notes
+verification = sync.verify_consistency()
+if not verification.is_consistent:
+    sync.repair(verification)
+```
+
+For complete API documentation, see the [Developer Guide](docs/DEVELOPER_GUIDE.md).
+
 ## Claude Code Plugin
 
 When used as a Claude Code plugin, the following slash commands are available:
@@ -102,27 +159,48 @@ make quality
 
 ## Configuration
 
-Environment variables (see `.env.example` for all options):
+### Core Settings
 
 | Variable | Description | Default |
 |----------|-------------|---------|
-| `MEMORY_PLUGIN_DATA_DIR` | Data directory path | `~/.local/share/memory-plugin/` |
-| `MEMORY_PLUGIN_GIT_NAMESPACE` | Git notes namespace | `refs/notes/mem` |
-| `MEMORY_PLUGIN_EMBEDDING_MODEL` | Embedding model name | `all-MiniLM-L6-v2` |
+| `MEMORY_PLUGIN_DATA_DIR` | Data directory for index and models | `~/.local/share/memory-plugin/` |
+| `MEMORY_PLUGIN_GIT_NAMESPACE` | Git notes ref prefix | `refs/notes/mem` |
+| `MEMORY_PLUGIN_EMBEDDING_MODEL` | Sentence-transformer model | `all-MiniLM-L6-v2` |
 | `MEMORY_PLUGIN_AUTO_CAPTURE` | Enable auto-capture hook | `false` |
 
 ### Hook Configuration
 
 | Variable | Description | Default |
 |----------|-------------|---------|
-| `HOOK_ENABLED` | Master switch for hooks | `true` |
+| `HOOK_ENABLED` | Master switch for all hooks | `true` |
 | `HOOK_SESSION_START_ENABLED` | Enable SessionStart context injection | `true` |
+| `HOOK_SESSION_START_INCLUDE_GUIDANCE` | Include response guidance templates | `true` |
+| `HOOK_SESSION_START_GUIDANCE_DETAIL` | Guidance level: minimal/standard/detailed | `standard` |
 | `HOOK_USER_PROMPT_ENABLED` | Enable signal detection in prompts | `false` |
 | `HOOK_POST_TOOL_USE_ENABLED` | Enable file-contextual memory injection | `true` |
+| `HOOK_POST_TOOL_USE_MIN_SIMILARITY` | Minimum similarity threshold | `0.6` |
+| `HOOK_POST_TOOL_USE_MAX_RESULTS` | Maximum memories to inject | `3` |
+| `HOOK_POST_TOOL_USE_AUTO_CAPTURE` | Auto-capture from written content | `true` |
 | `HOOK_PRE_COMPACT_ENABLED` | Enable auto-capture before compaction | `true` |
+| `HOOK_PRE_COMPACT_AUTO_CAPTURE` | Auto-capture without prompt | `true` |
+| `HOOK_PRE_COMPACT_PROMPT_FIRST` | Suggestion mode (show, don't capture) | `false` |
+| `HOOK_PRE_COMPACT_MIN_CONFIDENCE` | Minimum confidence for capture | `0.85` |
+| `HOOK_PRE_COMPACT_MAX_CAPTURES` | Maximum captures per compaction | `3` |
 | `HOOK_STOP_ENABLED` | Enable Stop hook processing | `true` |
+| `HOOK_STOP_SYNC_INDEX` | Sync index on session end | `true` |
+| `HOOK_STOP_PROMPT_UNCAPTURED` | Prompt for uncaptured content | `true` |
 | `HOOK_DEBUG` | Enable debug logging to stderr | `false` |
 
+### Performance Tuning
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `HOOK_SESSION_START_TOKEN_BUDGET` | Max tokens for context injection | `2000` |
+| `HOOK_POST_TOOL_USE_TIMEOUT` | Hook timeout in seconds | `5` |
+| `HOOK_PRE_COMPACT_TIMEOUT` | Hook timeout in seconds | `15` |
+
+See `.env.example` for the complete list of configuration options.
+
 ## Requirements
 
 - Python 3.11+

commands/capture.md

@@ -4,6 +4,46 @@ argument-hint: "[namespace] <summary> -- <content>"
 allowed-tools: ["Bash", "Write", "Read", "AskUserQuestion"]
 ---
 
+<help_check>
+## Help Check
+
+If `$ARGUMENTS` contains `--help` or `-h`:
+
+**Output this help and HALT (do not proceed further):**
+
+<help_output>
+```
+CAPTURE(1)                                           User Commands                                           CAPTURE(1)
+
+NAME
+    capture - Capture a memory (decision, learning, blocker, progress...
+
+SYNOPSIS
+    /memory:capture [namespace] <summary> -- <content>
+
+DESCRIPTION
+    Capture a memory (decision, learning, blocker, progress, etc.) to the git-backed memory system
+
+OPTIONS
+    --help, -h                Show this help message
+
+EXAMPLES
+    /memory:capture
+    /memory:capture <namespace>
+    /memory:capture --help
+
+SEE ALSO
+    /memory:* for related commands
+
+                                                                      CAPTURE(1)
+```
+</help_output>
+
+**After outputting help, HALT immediately. Do not proceed with command execution.**
+</help_check>
+
+---
+
 # /memory:capture - Capture a Memory
 
 Capture information to the git-backed memory system for later retrieval.
@@ -12,7 +52,7 @@ Capture information to the git-backed memory system for later retrieval.
 
 You will help the user capture a memory. The memory will be stored as a git note and indexed for semantic search.
 
-### Step 1: Parse the Arguments
+<step number="1" name="Parse the Arguments">
 
 **Arguments format**: `$ARGUMENTS`
 
@@ -31,14 +71,18 @@ If no namespace specified, auto-detect based on content patterns:
 - Contains "pattern", "recurring", "often" → `patterns`
 - Default → `learnings`
 
-### Step 2: Validate Content
+</step>
+
+<step number="2" name="Validate Content">
 
 If `$ARGUMENTS` is empty or very short (< 10 characters):
 - Use AskUserQuestion to prompt for the memory content
 - Question: "What would you like to capture?"
 - Provide examples for each memory type
 
-### Step 3: Capture the Memory
+</step>
+
+<step number="3" name="Capture the Memory">
 
 Use Bash to invoke the Python library:
 
@@ -69,7 +113,9 @@ Replace:
 - `$SUMMARY` with a one-line summary (max 100 chars, escape quotes)
 - `$CONTENT` with the full content (escape quotes)
 
-### Step 4: Confirm to User
+</step>
+
+<step number="4" name="Confirm to User">
 
 Show the result:
 ```
@@ -83,6 +129,8 @@ This memory will be available for recall in future sessions.
 Use `/memory:recall` to retrieve it.
 ```
 
+</step>
+
 ## Namespace Reference
 
 | Namespace | Use For | Example |
@@ -108,13 +156,15 @@ For structured captures, the library also provides:
 - `capture_pattern(summary, pattern_type, evidence, confidence)` - Patterns
 - `capture_review(spec, summary, findings, verdict)` - Code reviews
 
-## Error Handling
+<error_handling>
 
 If the capture fails:
 1. Check if we're in a git repository: `git rev-parse --git-dir`
 2. Check if the library is installed: `uv run python3 -c "import git_notes_memory"`
 3. Show helpful error message with recovery action
 
+</error_handling>
+
 ## Examples
 
 **User**: `/memory:capture decisions Use Redis for session storage -- Due to built-in expiration and cluster support`
@@ -131,9 +181,20 @@ If the capture fails:
 After successfully capturing a memory, remind the user:
 
 ```
-💡 **Pro tip**: You can capture memories inline using markers:
+**Pro tip**: You can capture memories inline using markers:
 - `[remember] <insight>` - Captures a learning
 - `[capture] <decision>` - Captures any type of memory
 - `@memory <content>` - Same as [capture]
 
 These markers work anywhere in your message and are automatically processed.
+```
+
+## Related Commands
+
+| Command | Description |
+|---------|-------------|
+| `/memory:recall` | Search and retrieve captured memories semantically |
+| `/memory:search` | Advanced search with filtering options |
+| `/memory:status` | View memory system statistics and health |
+| `/memory:sync` | Synchronize the index with git notes |
+| `/memory:validate` | Validate the memory system is working correctly |