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/LABELS.md

@@ -525,7 +525,6 @@ bd import -i .beads/issues.jsonl
 
 ## See Also
 
-- [README.md](README.md) - Main documentation
-- [AGENTS.md](AGENTS.md) - AI agent integration guide
-- [AGENTS.md](AGENTS.md) - Team workflow patterns
+- [README.md](../README.md) - Main documentation
+- [AGENTS.md](../AGENTS.md) - AI agent integration guide
 - [ADVANCED.md](ADVANCED.md) - JSONL format details