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 ⚠️ Outdated frontend README (generic Vite template)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

# 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

# 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):

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)

   # 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)