ai-notes/documentation-audit-2025-11-27.md

# Documentation Audit Report - Document-MCP
**Date**: 2025-11-27
**Purpose**: Pre-release audit for accuracy, completeness, and professionalism

## Executive Summary

The Document-MCP project documentation is **generally accurate and comprehensive**, but requires several critical fixes before public release:

### Critical Issues (MUST FIX)
1. ❌ **Personal information exposed** in DEPLOY_TO_HF.md (username: YOUR_USERNAME)
2. ❌ **Placeholder URLs** not replaced (YOUR_REPO, YOUR_USERNAME)
3. ❌ **Missing LICENSE file** (mentioned in README but doesn't exist)
4. ❌ **Inaccurate route count** in CLAUDE.md (claims 11 routes, actual is 18)
5. ❌ **Incomplete .env.example** (missing several required variables)

### Minor Issues (SHOULD FIX)
1. ⚠️ **Outdated frontend README** (generic Vite template)
2. ⚠️ **Empty backend README** (only 1 line)
3. ⚠️ **GEMINI.md is auto-generated** and out of sync
4. ⚠️ **Inconsistent command format** in CLAUDE.md (uses `main:app` but file is at `src.api.main:app`)

---

## Detailed Findings

### 1. README.md (Root)
**Location**: `$PROJECT_ROOT/README.md`

**Status**: ✅ Mostly Good

**Strengths**:
- Clear project description
- Good feature list
- Well-structured sections
- Includes demo mode warning

**Issues**:
1. **Line 101**: `https://github.com/YOUR_REPO/Document-MCP/blob/main/DEPLOYMENT.md` - placeholder URL not replaced
2. **Line 112**: References LICENSE file that doesn't exist
3. Missing repository URL in frontmatter (lines 1-9)

**Recommendations**:
- Replace `YOUR_REPO` with actual GitHub username/org
- Create LICENSE file (MIT as stated)
- Add actual repository URL to YAML frontmatter

---

### 2. CLAUDE.md
**Location**: `$PROJECT_ROOT/CLAUDE.md`

**Status**: ⚠️ Needs Updates

**Strengths**:
- Comprehensive technical documentation
- Excellent architecture descriptions
- Detailed command examples
- Good MCP configuration examples

**Inaccuracies Found**:

#### Line 34: Incorrect uvicorn command
```bash
# CLAUDE.md says:
uv run uvicorn main:app --reload --host 0.0.0.0 --port 8000

# Should be (verified against backend/main.py):
uv run uvicorn src.api.main:app --reload --host 0.0.0.0 --port 8000
# OR simply:
cd backend && uv run python main.py
```

#### Line 110: Incorrect route count
```
# Claims:
11 routes: auth, notes CRUD, search, backlinks, tags, index health/rebuild

# Actual count: 18 routes across 7 files
- auth.py: 4 routes
- notes.py: 5 routes
- search.py: 3 routes
- index.py: 2 routes
- graph.py: 1 route
- demo.py: 1 route
- system.py: 2 routes
```

#### Lines 88-93: Missing models
**Claims these models exist**:
- `note.py` ✅ EXISTS
- `user.py` ✅ EXISTS
- `search.py` ✅ EXISTS
- `index.py` ✅ EXISTS
- `auth.py` ✅ EXISTS
- `graph.py` ✅ EXISTS (not mentioned but exists)

**Recommendation**: Add `graph.py` to the list.

#### Line 112: Missing route files
**Claims**: "7 tools: list, read, write, delete, search, backlinks, tags"

**Actual MCP tools**: Should verify this count against actual MCP server implementation.

#### Line 79: Database init command inaccuracy
```bash
# Claims:
uv run python -c "from src.services.database import DatabaseService; DatabaseService().init_schema()"

# Actual method is:
DatabaseService().initialize()
# NOT init_schema()
```

**Verified from `$PROJECT_ROOT/backend/src/services/database.py`**:
- Line 92: Method is `def initialize(self, statements: Iterable[str] | None = None)`
- No `init_schema()` method exists

---

### 3. DEPLOYMENT.md
**Location**: `$PROJECT_ROOT/DEPLOYMENT.md`

**Status**: ✅ Good, Minor Placeholders

**Issues**:
1. Multiple instances of `YOUR_USERNAME` placeholder (appropriate for public doc)
2. All technical instructions verified as accurate

**Recommendations**:
- Keep `YOUR_USERNAME` as placeholder (this is correct for public docs)
- Maybe add a note at the top: "Replace YOUR_USERNAME with your HuggingFace username"

---

### 4. DEPLOY_TO_HF.md ⚠️ CRITICAL
**Location**: `$PROJECT_ROOT/DEPLOY_TO_HF.md`

**Status**: ❌ Contains Personal Information

**CRITICAL ISSUES**:
1. **Line 6**: `hf-space` → `https://huggingface.co/spaces/YOUR_USERNAME/Document-MCP`
2. **Line 12**: `git config credential.helper '!f() { echo "username=YOUR_USERNAME"; ...`
3. **Line 32**: `huggingface-cli upload YOUR_USERNAME/Document-MCP`
4. **Line 40**: `git clone https://huggingface.co/spaces/YOUR_USERNAME/Document-MCP`

**Recommendation**:
- **DELETE this file** before public release (it's personal deployment notes)
- OR replace all instances of `YOUR_USERNAME` with `YOUR_USERNAME`

---

### 5. .env.example
**Location**: `$PROJECT_ROOT/.env.example`

**Status**: ❌ Incomplete

**Current Contents** (only 4 variables):
```env
JWT_SECRET_KEY=change-me
HF_OAUTH_CLIENT_ID=your-hf-client-id
HF_OAUTH_CLIENT_SECRET=your-hf-client-secret
VAULT_BASE_PATH=./data/vaults
```

**Missing Variables** (referenced in CLAUDE.md and code):
- `MODE` (local or space)
- `DB_PATH` (SQLite database location)
- `LOCAL_USER_ID` (default user for local mode)
- `HF_SPACE_HOST` (for HF Space deployments)

**Recommendation**: Add comprehensive .env.example with all variables documented.

---

### 6. backend/README.md
**Location**: `$PROJECT_ROOT/backend/README.md`

**Status**: ❌ Nearly Empty (1 line)

**Current State**: File exists but has no meaningful content.

**Recommendation**: Add backend-specific documentation:
- Installation instructions
- Development setup
- Testing guide
- Service architecture overview

---

### 7. frontend/README.md
**Location**: `$PROJECT_ROOT/frontend/README.md`

**Status**: ⚠️ Generic Vite Template

**Current State**: Still contains the default Vite + React template README.

**Recommendation**: Replace with project-specific frontend documentation:
- Component architecture
- Development workflow
- Build instructions
- UI/UX guidelines

---

### 8. GEMINI.md
**Location**: `$PROJECT_ROOT/GEMINI.md`

**Status**: ⚠️ Auto-generated, Out of Sync

**Issues**:
- Clearly auto-generated from SpecKit
- Contains malformed commands (e.g., "cd src [ONLY COMMANDS FOR ACTIVE TECHNOLOGIES]")
- Last updated 2025-11-25 (2 days old)
- Doesn't match actual project structure

**Recommendation**:
- **DELETE** or move to `.specify/` internal folder
- Not useful for public documentation

---

### 9. LICENSE File
**Status**: ❌ MISSING

**Referenced in**:
- README.md line 112: "MIT License - See LICENSE file for details"
- README.md line 8: `license: mit`

**Recommendation**: Create LICENSE file with MIT license text.

---

### 10. Package Metadata

#### backend/pyproject.toml
**Location**: `$PROJECT_ROOT/backend/pyproject.toml`

**Status**: ⚠️ Incomplete Metadata

**Issues**:
- Line 1: `name = "Documentation-MCP"` (inconsistent with project name "Document-MCP")
- Line 4: `description = "Add your description here"` (placeholder)
- Line 5: `readme = "README.md"` (points to empty README)

**Recommendations**:
- Fix name to `"document-mcp"`
- Add proper description
- Add author, repository URL, keywords

#### frontend/package.json
**Location**: `$PROJECT_ROOT/frontend/package.json`

**Status**: ⚠️ Generic Template

**Issues**:
- Line 2: `"name": "frontend"` (too generic)
- Line 3: `"private": true` (correct for non-published packages)
- Line 5: `"version": "0.0.0"` (should match backend version)
- Missing description, author, repository fields

**Recommendations**:
- Change name to `"document-mcp-frontend"`
- Add proper metadata matching backend

---

## File Structure Verification

### Backend Structure ✅
Verified actual structure matches CLAUDE.md claims:

```
backend/src/
├── models/          ✅ (7 files: auth, graph, index, note, search, user, __init__)
├── services/        ✅ (7 files: auth, config, database, indexer, seed, vault, __init__)
├── api/
│   ├── routes/      ✅ (8 files: auth, demo, graph, index, notes, search, system, __init__)
│   └── middleware/  ✅
└── mcp/
    └── server.py    ✅
```

### Frontend Structure ✅
```
frontend/src/
├── components/      ✅ (GraphView, NoteViewer, NoteEditor, DirectoryTree, etc.)
├── lib/            ✅
├── services/       ✅
└── types/          ✅
```

---

## Command Verification

### Backend Commands (from CLAUDE.md)

| Command | Line | Status | Notes |
|---------|------|--------|-------|
| `uv venv` | 26 | ✅ Works | Verified |
| `uv pip install -e .` | 28 | ✅ Works | Verified |
| `uv run uvicorn main:app` | 34 | ❌ Wrong | Should be `src.api.main:app` |
| `uv run python src/mcp/server.py` | 37 | ✅ Works | Verified |
| `uv run pytest` | 43 | ✅ Works | Requires dev deps |

### Frontend Commands

| Command | Line | Status |
|---------|------|--------|
| `npm install` | 57 | ✅ Works |
| `npm run dev` | 60 | ✅ Works |
| `npm run build` | 63 | ✅ Works |
| `npm run lint` | 66 | ✅ Works |

---

## Architecture Verification

### SQLite Schema ✅
Verified against `$PROJECT_ROOT/backend/src/services/database.py`:

**CLAUDE.md claims 5 tables**:
1. `note_metadata` ✅ (lines 15-26)
2. `note_fts` ✅ (lines 33-41)
3. `note_tags` ✅ (lines 43-49)
4. `note_links` ✅ (lines 53-61)
5. `index_health` ✅ (lines 66-72)

**All verified as accurate!**

### API Routes Count ❌
**CLAUDE.md Line 110 claims**: "11 routes: auth, notes CRUD, search, backlinks, tags, index health/rebuild"

**Actual count**: 18 routes across 7 router files
- Not technically wrong (may be counting logical endpoints vs. HTTP routes)
- But confusing and should be clarified

---

## Links Audit

### Internal Links
All internal file references in CLAUDE.md verified:
- ✅ `backend/src/models/`
- ✅ `backend/src/services/`
- ✅ `backend/src/api/routes/`
- ✅ `.env.example`

### External Links
No broken external links found in:
- README.md
- DEPLOYMENT.md
- CLAUDE.md

### Placeholder Links ❌
- `https://github.com/YOUR_REPO/Document-MCP` (README.md)
- Multiple `YOUR_USERNAME` placeholders (appropriate for templates)

---

## Recommendations by Priority

### 🔴 CRITICAL (Must fix before public release)

1. **Create LICENSE file** (MIT as stated)
   ```bash
   # Add MIT license text to LICENSE file
   ```

2. **Remove/anonymize DEPLOY_TO_HF.md**
   - Delete entirely OR
   - Replace `YOUR_USERNAME` with `YOUR_USERNAME`

3. **Fix placeholder URLs in README.md**
   - Replace `YOUR_REPO` with actual GitHub username/org

4. **Fix .env.example**
   - Add all missing environment variables
   - Add comments explaining each variable

5. **Fix CLAUDE.md inaccuracies**:
   - Line 34: Correct uvicorn command
   - Line 79: Fix `init_schema()` → `initialize()`
   - Line 110: Clarify route count or update to 18

### 🟡 IMPORTANT (Should fix)

6. **Update backend/pyproject.toml**
   - Fix name: `Documentation-MCP` → `document-mcp`
   - Add proper description
   - Add author, repository, keywords

7. **Replace frontend/README.md**
   - Remove Vite template content
   - Add project-specific frontend docs

8. **Create backend/README.md**
   - Installation guide
   - Testing instructions
   - Architecture overview

9. **Delete or hide GEMINI.md**
   - Auto-generated, not useful publicly
   - Move to `.specify/` if needed internally

### 🟢 NICE TO HAVE (Optional improvements)

10. **Add CONTRIBUTING.md**
    - Contribution guidelines
    - Code style requirements
    - PR process

11. **Add CHANGELOG.md**
    - Version history
    - Breaking changes
    - Migration guides

12. **Expand docs/ folder**
    - Architecture diagrams
    - API reference
    - Deployment guides per platform

---

## Code Quality Cross-Check

### Python Code ✅
- All imports in CLAUDE.md verified working
- Service layer structure matches documentation
- Database schema matches DDL statements

### TypeScript/React Code ✅
- Component hierarchy matches CLAUDE.md
- Dependencies in package.json match documentation

### MCP Integration ✅
- Server file exists at documented location
- Transport modes (STDIO/HTTP) documented correctly
- Configuration examples are accurate

---

## Security & Privacy Check

### Exposed Information ❌
- **DEPLOY_TO_HF.md**: Contains username `YOUR_USERNAME`
- No API keys or secrets exposed ✅
- No real JWT tokens in examples ✅

### Placeholder Patterns ✅
- Appropriate use of `YOUR_USERNAME` in public docs
- Example tokens are clearly fake
- Environment variables use placeholder values

---

## Conclusion

The Document-MCP documentation is **well-written and comprehensive** but needs **critical fixes before public release**:

### Must-Fix Checklist
- [ ] Create LICENSE file
- [ ] Remove/anonymize DEPLOY_TO_HF.md
- [ ] Replace `YOUR_REPO` placeholder in README.md
- [ ] Expand .env.example with all variables
- [ ] Fix CLAUDE.md command inaccuracies
- [ ] Update backend/pyproject.toml metadata
- [ ] Replace generic frontend/README.md
- [ ] Delete or move GEMINI.md

### Quality Score: 7.5/10
**Breakdown**:
- Technical accuracy: 8/10 (few minor inaccuracies)
- Completeness: 7/10 (missing LICENSE, sparse READMEs)
- Professionalism: 6/10 (personal info, placeholders)
- Usability: 9/10 (clear, well-organized)

**Estimated time to fix**: 2-3 hours

---

## Confidence Assessment

**Confidence Level**: 9/10

**Reasoning**:
- Manually verified file structure against documentation
- Tested import paths and commands
- Cross-referenced schema definitions
- Counted actual routes in codebase
- Found both critical and minor issues
- Some uncertainty remains on MCP tool count (need to verify against actual MCP server implementation)