feat: add optional features for large vaults and SSL certificate support

[kevincormier-toast]

Feature Additions: Enhanced Configuration and Debugging

Apologies for the Multi-Feature PR

I apologize for submitting multiple features in one PR - I realize this isn't ideal for review. I'm happy to split this into separate PRs if you prefer. Each feature is in its own commit which should make review easier, but please let me know if you'd like me to split them up.

Summary

This PR adds several optional features to improve usability for different vault sizes and deployment scenarios:

1. Optional Journaling Tool - Agent reflection and rubber duck debugging
2. Patch Content Tool Improvements - Better documentation to prevent common errors
3. Disable Simple Search - For large vaults that overwhelm token limits
4. Custom SSL Certificates - Use self-signed certs without system keychain
5. Debug Logging - Troubleshoot connection and SSL issues

All features are opt-in via environment variables and maintain full backward compatibility.

---

1. Optional Journaling Tool (62be425)

Problem: Agents working on complex tasks benefit from articulating their thinking (rubber duck debugging), and cross-session continuity requires capturing the messy reality of development.

Solution: Adds obsidian_journal_entry tool (gated behind OBSIDIAN_ENABLE_JOURNALING=true) that automates timestamps, formatting, and file organization for agent reflection logs.

Documentation: Extensive guidance in JOURNALING.md on getting value from agent journaling.

Why opt-in: Requires thoughtful prompting to be valuable - not useful for everyone.

---

2. Patch Content Tool Improvements (46f983b)

Problem: The patch_content tool's heading path requirements caused frequent errors - users weren't building full paths from h1 down.

Solution: Enhanced tool description with explicit instructions and examples showing correct vs incorrect usage.

Impact: Reduces agent errors and user frustration with heading-based patches.

---

3. Disable Simple Search (76bfe4c)

Problem: For large vaults, simple_search returns excessive context that can overwhelm token limits, making the tool unusable.

Solution: Add OBSIDIAN_DISABLE_SIMPLE_SEARCH=true to hide the simple search tool while keeping complex search available.

Why opt-in: Most users benefit from simple search - only large vaults need this.

---

4. Custom SSL Certificate Support (bbf03a0)

Problem: The Obsidian Local REST API uses self-signed certificates. Currently, users must either:

• Add the cert to system keychain and mark it globally trusted (security risk)
• Disable SSL verification entirely (verify=False)

Solution: Support custom SSL certificates without system keychain:

• OBSIDIAN_SSL_CERT_BASE64 - Base64-encoded certificate (recommended)
• OBSIDIAN_SSL_CERT_PATH - Path to certificate file

Benefits:

• Certificate scoped to this connection only
• No global trust required
• Automatic temp file cleanup
• Clear error messages for invalid configs

---

5. Debug Logging (5f9f817)

Problem: MCP servers use stdio for communication, making it extremely difficult to debug connection issues, SSL errors, or configuration problems.

Solution: Add OBSIDIAN_DEBUG_LOG=/path/to/debug.log to write diagnostic information to a separate file:

• Environment configuration and SSL cert setup
• All MCP tool calls with request/response details
• API requests with URLs and verify_ssl settings
• Full stack traces for errors
• Feature flag status

Why needed: This was essential for debugging the SSL certificate feature and helped identify a real issue where tilde expansion in paths failed silently.

Documentation: Added warning about using full paths instead of ~ in configs.

---

Testing

All features tested with:

• Syntax validation (python3 -m py_compile)
• Import validation in venv
• Backward compatibility (all env vars optional)
• Debug logging output verification

Breaking Changes

None - all features are opt-in and maintain full backward compatibility.

---

Again, I apologize for the multi-feature PR. Please let me know if you'd like me to:

1. Split this into separate PRs (I can do this quickly)
2. Remove any features you don't want
3. Make any changes to the implementation or documentation

Thank you for maintaining this excellent MCP server!