docs: fix broken relative links across documentation

Fixes 46 broken relative links across 20 documentation files in docs/.

Changes:
- Added ../ prefix for root files (README.md, AGENTS.md)
- Removed ../ prefix for sibling docs files
- Removed dead links to non-existent files
- Fixed subdirectory paths

Based on PR #574 by chrisvaillancourt.

Co-Authored-By: Chris Vaillancourt <chrisvaillancourt@users.noreply.github.com>

docs/adr/002-agent-mail-integration.md

@@ -220,10 +220,6 @@ Total latency: <100ms (vs 2000-5000ms with git-only)
 ## References
 
 - [MCP Agent Mail Repository](https://github.com/Dicklesworthstone/mcp_agent_mail)
-- [bd-spmx Epic](../../.beads/beads.db) - Investigation & Proof of Concept
-- [bd-6hji](../../.beads/beads.db) - File Reservation Testing
-- [bd-htfk](../../.beads/beads.db) - Latency Benchmarking
-- [Latency Results](../../latency_results.md)
 
 ## Decision Outcome