diff --git a/docs/ADAPTIVE_IDS.md b/docs/ADAPTIVE_IDS.md
index 407f7add..6b82824b 100644
--- a/docs/ADAPTIVE_IDS.md
+++ b/docs/ADAPTIVE_IDS.md
@@ -194,6 +194,5 @@ Potential improvements (not yet implemented):
 
 ## Related
 
-- [Hash ID Design](HASH_ID_DESIGN.md) - Overview of hash-based IDs
 - [Migration Guide](../README.md#migration) - Converting from sequential to hash IDs
-- [Configuration](../CONFIG.md) - All configuration options
+- [Configuration](CONFIG.md) - All configuration options
diff --git a/docs/ADVANCED.md b/docs/ADVANCED.md
index b1f4e10c..8ef31796 100644
--- a/docs/ADVANCED.md
+++ b/docs/ADVANCED.md
@@ -365,7 +365,7 @@ Understanding the role of each component:
 
 ## Next Steps
 
-- **[README.md](README.md)** - Core features and quick start
+- **[README.md](../README.md)** - Core features and quick start
 - **[TROUBLESHOOTING.md](TROUBLESHOOTING.md)** - Common issues and solutions
 - **[FAQ.md](FAQ.md)** - Frequently asked questions
 - **[CONFIG.md](CONFIG.md)** - Configuration system guide
diff --git a/docs/AGENT_MAIL.md b/docs/AGENT_MAIL.md
index 6f8fd137..e0070a9a 100644
--- a/docs/AGENT_MAIL.md
+++ b/docs/AGENT_MAIL.md
@@ -511,8 +511,6 @@ jobs:
 
 - [ADR 002: Agent Mail Integration](adr/002-agent-mail-integration.md)
 - [Agent Mail Repository](https://github.com/Dicklesworthstone/mcp_agent_mail)
-- [Integration Status](../AGENT_MAIL_INTEGRATION_STATUS.md)
-- [Latency Benchmark Results](../latency_results.md)
 - [Python Agent Example](../examples/python-agent/)
 
 ## Contributing
diff --git a/docs/AGENT_MAIL_DEPLOYMENT.md b/docs/AGENT_MAIL_DEPLOYMENT.md
index 35d57640..fdd80233 100644
--- a/docs/AGENT_MAIL_DEPLOYMENT.md
+++ b/docs/AGENT_MAIL_DEPLOYMENT.md
@@ -623,7 +623,7 @@ After successful deployment:
 - **Main Guide**: [AGENT_MAIL_MULTI_WORKSPACE_SETUP.md](AGENT_MAIL_MULTI_WORKSPACE_SETUP.md)
 - **Quick Start**: [AGENT_MAIL_QUICKSTART.md](AGENT_MAIL_QUICKSTART.md)
 - **Architecture**: [AGENT_MAIL.md](AGENT_MAIL.md)
-- **ADR**: [adr/002-agent-mail-integration.md](../adr/002-agent-mail-integration.md)
+- **ADR**: [adr/002-agent-mail-integration.md](adr/002-agent-mail-integration.md)
 
 ## Timeline Estimate
 
diff --git a/docs/AGENT_MAIL_QUICKSTART.md b/docs/AGENT_MAIL_QUICKSTART.md
index bb72518e..c932e63d 100644
--- a/docs/AGENT_MAIL_QUICKSTART.md
+++ b/docs/AGENT_MAIL_QUICKSTART.md
@@ -434,7 +434,6 @@ except Exception:
 1. **Read the full guide**: [AGENT_MAIL.md](AGENT_MAIL.md)
 2. **Try the Python example**: [examples/python-agent/AGENT_MAIL_EXAMPLE.md](../examples/python-agent/AGENT_MAIL_EXAMPLE.md)
 3. **Review the ADR**: [adr/002-agent-mail-integration.md](adr/002-agent-mail-integration.md)
-4. **Check out benchmarks**: [../latency_results.md](../latency_results.md)
 
 ## Getting Help
 
diff --git a/docs/CLAUDE.md b/docs/CLAUDE.md
index 63043ebb..047e68fd 100644
--- a/docs/CLAUDE.md
+++ b/docs/CLAUDE.md
@@ -6,7 +6,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 **beads** (command: `bd`) is a git-backed issue tracker for AI-supervised coding workflows. We dogfood our own tool.
 
-**IMPORTANT**: See [AGENTS.md](AGENTS.md) for complete workflow instructions, bd commands, and development guidelines.
+**IMPORTANT**: See [AGENTS.md](../AGENTS.md) for complete workflow instructions, bd commands, and development guidelines.
 
 ## Architecture Overview
 
diff --git a/docs/CLI_REFERENCE.md b/docs/CLI_REFERENCE.md
index fb01f911..1fddf295 100644
--- a/docs/CLI_REFERENCE.md
+++ b/docs/CLI_REFERENCE.md
@@ -555,5 +555,5 @@ bd sync  # Force immediate sync, bypass debounce
 - [AGENTS.md](../AGENTS.md) - Main agent workflow guide
 - [DAEMON.md](DAEMON.md) - Daemon management and event-driven mode
 - [GIT_INTEGRATION.md](GIT_INTEGRATION.md) - Git workflows and merge strategies
-- [LABELS.md](../LABELS.md) - Label system guide
+- [LABELS.md](LABELS.md) - Label system guide
 - [README.md](../README.md) - User documentation
diff --git a/docs/COLLISION_MATH.md b/docs/COLLISION_MATH.md
index 870aa705..6cd87599 100644
--- a/docs/COLLISION_MATH.md
+++ b/docs/COLLISION_MATH.md
@@ -143,5 +143,4 @@ This generates the tables above and shows adaptive scaling strategy for any thre
 ## Related Documentation
 
 - [ADAPTIVE_IDS.md](ADAPTIVE_IDS.md) - Configuration and usage guide
-- [HASH_ID_DESIGN.md](HASH_ID_DESIGN.md) - Overall hash ID design rationale
-- [CONFIG.md](../CONFIG.md) - All configuration options
+- [CONFIG.md](CONFIG.md) - All configuration options
diff --git a/docs/CONFIG.md b/docs/CONFIG.md
index 4898fc33..e93f45bb 100644
--- a/docs/CONFIG.md
+++ b/docs/CONFIG.md
@@ -216,7 +216,7 @@ bd config set max_collision_prob "0.01"
 bd config set min_hash_length "5"
 ```
 
-See [docs/ADAPTIVE_IDS.md](docs/ADAPTIVE_IDS.md) for detailed documentation.
+See [ADAPTIVE_IDS.md](ADAPTIVE_IDS.md) for detailed documentation.
 
 ### Example: Export Error Handling
 
@@ -460,6 +460,5 @@ External integration scripts can read configuration to sync with Jira, Linear, G
 
 ## See Also
 
-- [README.md](README.md) - Main documentation
+- [README.md](../README.md) - Main documentation
 - [EXTENDING.md](EXTENDING.md) - Database schema and compaction config
-- [examples/integrations/](examples/integrations/) - Integration examples
diff --git a/docs/DAEMON.md b/docs/DAEMON.md
index 3852dbb3..c059e20a 100644
--- a/docs/DAEMON.md
+++ b/docs/DAEMON.md
@@ -436,7 +436,7 @@ rm .beads/.exclusive-lock
 - CI/CD pipelines (controlled sync timing)
 - Testing frameworks (isolated test runs)
 
-See [EXCLUSIVE_LOCK.md](../EXCLUSIVE_LOCK.md) for complete documentation.
+See [EXCLUSIVE_LOCK.md](EXCLUSIVE_LOCK.md) for complete documentation.
 
 ## Common Daemon Issues
 
@@ -542,6 +542,6 @@ bd daemons killall
 ## See Also
 
 - [AGENTS.md](../AGENTS.md) - Main agent workflow guide
-- [EXCLUSIVE_LOCK.md](../EXCLUSIVE_LOCK.md) - External tool integration
+- [EXCLUSIVE_LOCK.md](EXCLUSIVE_LOCK.md) - External tool integration
 - [GIT_INTEGRATION.md](GIT_INTEGRATION.md) - Git workflow and merge strategies
 - [commands/daemons.md](../commands/daemons.md) - Daemon command reference
diff --git a/docs/EXTENDING.md b/docs/EXTENDING.md
index e7ffa1a0..1bc1fdd1 100644
--- a/docs/EXTENDING.md
+++ b/docs/EXTENDING.md
@@ -712,6 +712,6 @@ This pattern scales from simple scripts to complex orchestrators like VC.
 
 ## See Also
 
-- [README.md](README.md) - Complete bd documentation
+- [README.md](../README.md) - Complete bd documentation
 - Run `bd quickstart` - Interactive tutorial
 - Check out VC's implementation at `github.com/steveyegge/vc` for a real-world example
diff --git a/docs/FAQ.md b/docs/FAQ.md
index ec851360..929721b1 100644
--- a/docs/FAQ.md
+++ b/docs/FAQ.md
@@ -302,7 +302,7 @@ We don't have automated migration tools yet, but you can:
 2. Write a simple script to convert to bd's JSONL format
 3. Import with `bd import -i issues.jsonl`
 
-See [examples/](examples/) for scripting patterns. Contributions welcome!
+See [examples/](../examples/) for scripting patterns. Contributions welcome!
 
 ### Can I export back to GitHub Issues / Jira?
 
@@ -463,15 +463,15 @@ bd import -i .beads/issues.jsonl
 
 ### Where can I get more help?
 
-- **Documentation**: [README.md](README.md), [QUICKSTART.md](QUICKSTART.md), [ADVANCED.md](ADVANCED.md)
+- **Documentation**: [README.md](../README.md), [QUICKSTART.md](QUICKSTART.md), [ADVANCED.md](ADVANCED.md)
 - **Troubleshooting**: [TROUBLESHOOTING.md](TROUBLESHOOTING.md)
-- **Examples**: [examples/](examples/)
+- **Examples**: [examples/](../examples/)
 - **GitHub Issues**: [Report bugs or request features](https://github.com/steveyegge/beads/issues)
 - **GitHub Discussions**: [Ask questions](https://github.com/steveyegge/beads/discussions)
 
 ### How can I contribute?
 
-Contributions are welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for:
+Contributions are welcome! See [CONTRIBUTING.md](../CONTRIBUTING.md) for:
 
 - Code contribution guidelines
 - How to run tests
diff --git a/docs/INSTALLING.md b/docs/INSTALLING.md
index c566121c..e218f058 100644
--- a/docs/INSTALLING.md
+++ b/docs/INSTALLING.md
@@ -210,7 +210,7 @@ Add to your MCP settings:
 - ❌ Higher context overhead (MCP schemas add 10-50k tokens)
 - ❌ Additional latency from MCP protocol
 
-See [integrations/beads-mcp/README.md](integrations/beads-mcp/README.md) for detailed MCP server documentation.
+See [integrations/beads-mcp/README.md](../integrations/beads-mcp/README.md) for detailed MCP server documentation.
 
 ## Verifying Installation
 
@@ -286,9 +286,9 @@ See the "Claude Code Plugin" section above for alternative installation methods
 After installation:
 
 1. **Initialize a project**: `cd your-project && bd init`
-2. **Configure your agent**: Add bd instructions to `AGENTS.md` (see [README.md](README.md#quick-start))
+2. **Configure your agent**: Add bd instructions to `AGENTS.md` (see [README.md](../README.md#quick-start))
 3. **Learn the basics**: Run `bd quickstart` for an interactive tutorial
-4. **Explore examples**: Check out the [examples/](examples/) directory
+4. **Explore examples**: Check out the [examples/](../examples/) directory
 
 ## Updating bd
 
diff --git a/docs/LABELS.md b/docs/LABELS.md
index 34c74aed..0e8b7045 100644
--- a/docs/LABELS.md
+++ b/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
diff --git a/docs/MULTI_REPO_MIGRATION.md b/docs/MULTI_REPO_MIGRATION.md
index 5d6f6e60..a404a0f1 100644
--- a/docs/MULTI_REPO_MIGRATION.md
+++ b/docs/MULTI_REPO_MIGRATION.md
@@ -10,7 +10,7 @@ This guide helps you adopt beads' multi-repo workflow for OSS contributions, tea
 - [Multi-Phase Development](#multi-phase-development) - Separate repos per phase
 - [Multiple Personas](#multiple-personas) - Architect vs. implementer separation
 
-**New to beads?** See [QUICKSTART.md](../QUICKSTART.md) first.
+**New to beads?** See [QUICKSTART.md](QUICKSTART.md) first.
 
 ## What is Multi-Repo Mode?
 
@@ -398,7 +398,7 @@ bd list --json
 
 **Problem:** Multiple repos modifying same JSONL file.
 
-**Solution:** See [TROUBLESHOOTING.md](../TROUBLESHOOTING.md#git-merge-conflicts) and consider [beads-merge](https://github.com/neongreen/mono/tree/main/beads-merge) tool.
+**Solution:** See [TROUBLESHOOTING.md](TROUBLESHOOTING.md#git-merge-conflicts) and consider [beads-merge](https://github.com/neongreen/mono/tree/main/beads-merge) tool.
 
 ### Discovered issues in wrong repository
 
@@ -475,13 +475,13 @@ bd create "Issue" -p 1
 ## Next Steps
 
 - **CLI Reference:** See [README.md](../README.md) for command details
-- **Configuration Guide:** See [CONFIG.md](../CONFIG.md) for all config options
-- **Troubleshooting:** See [TROUBLESHOOTING.md](../TROUBLESHOOTING.md)
+- **Configuration Guide:** See [CONFIG.md](CONFIG.md) for all config options
+- **Troubleshooting:** See [TROUBLESHOOTING.md](TROUBLESHOOTING.md)
 - **Multi-Repo Internals:** See [MULTI_REPO_HYDRATION.md](MULTI_REPO_HYDRATION.md) and [ROUTING.md](ROUTING.md)
 
 ## Related Issues
 
-- [bd-8rd](/.beads/beads.jsonl#bd-8rd) - Migration and onboarding epic
-- [bd-mlcz](/.beads/beads.jsonl#bd-mlcz) - `bd migrate` command (planned)
-- [bd-kla1](/.beads/beads.jsonl#bd-kla1) - `bd init --contributor` wizard ✅ implemented
-- [bd-twlr](/.beads/beads.jsonl#bd-twlr) - `bd init --team` wizard ✅ implemented
+- `bd-8rd` - Migration and onboarding epic
+- `bd-mlcz` - `bd migrate` command (planned)
+- `bd-kla1` - `bd init --contributor` wizard ✅ implemented
+- `bd-twlr` - `bd init --team` wizard ✅ implemented
diff --git a/docs/QUICKSTART.md b/docs/QUICKSTART.md
index bd4f472e..2089c4a0 100644
--- a/docs/QUICKSTART.md
+++ b/docs/QUICKSTART.md
@@ -260,4 +260,4 @@ See [DAEMON.md](DAEMON.md) for complete daemon management guide.
 - Search issues: `./bd list --status open`
 - Detect cycles: `./bd dep cycles`
 
-See [README.md](README.md) for full documentation.
+See [README.md](../README.md) for full documentation.
diff --git a/docs/RELEASING.md b/docs/RELEASING.md
index 65433a8b..fe7f0528 100644
--- a/docs/RELEASING.md
+++ b/docs/RELEASING.md
@@ -12,7 +12,7 @@ Use the fully automated release script:
 
 This does **everything**: version bump, tests, git tag, Homebrew update, and local installation.
 
-See [scripts/README.md](scripts/README.md#releasesh--the-easy-button) for details.
+See [scripts/README.md](../scripts/README.md#releasesh--the-easy-button) for details.
 
 ---
 
@@ -129,7 +129,7 @@ uv build
 TWINE_USERNAME=__token__ TWINE_PASSWORD=pypi-... uv tool run twine upload dist/*
 ```
 
-See [integrations/beads-mcp/PYPI.md](integrations/beads-mcp/PYPI.md) for detailed PyPI instructions.
+See [integrations/beads-mcp/PYPI.md](../integrations/beads-mcp/PYPI.md) for detailed PyPI instructions.
 
 ### 3. Update Homebrew Formula
 
@@ -292,6 +292,6 @@ Set up API token at https://pypi.org/manage/account/token/ and use `__token__` a
 
 ## Related Documentation
 
-- [CHANGELOG.md](CHANGELOG.md) - Release history
-- [scripts/README.md](scripts/README.md) - Version bump script details
-- [integrations/beads-mcp/PYPI.md](integrations/beads-mcp/PYPI.md) - Detailed PyPI guide
+- [CHANGELOG.md](../CHANGELOG.md) - Release history
+- [scripts/README.md](../scripts/README.md) - Version bump script details
+- [integrations/beads-mcp/PYPI.md](../integrations/beads-mcp/PYPI.md) - Detailed PyPI guide
diff --git a/docs/TROUBLESHOOTING.md b/docs/TROUBLESHOOTING.md
index a810814f..9360bfb5 100644
--- a/docs/TROUBLESHOOTING.md
+++ b/docs/TROUBLESHOOTING.md
@@ -209,7 +209,7 @@ bd config set import.orphan_handling "strict"
 - Check for orphans before cleanup: `bd list --id bd-abc.*`
 - Review impact before deleting epic/parent issues
 
-See [docs/CONFIG.md](docs/CONFIG.md#example-import-orphan-handling) for complete configuration documentation.
+See [CONFIG.md](CONFIG.md#example-import-orphan-handling) for complete configuration documentation.
 
 ### Database corruption
 
@@ -524,7 +524,7 @@ bd ready
 ps aux | grep "bd daemon"
 ```
 
-See [integrations/beads-mcp/README.md](integrations/beads-mcp/README.md) for MCP-specific troubleshooting.
+See [integrations/beads-mcp/README.md](../integrations/beads-mcp/README.md) for MCP-specific troubleshooting.
 
 ### Sandboxed environments (Codex, Claude Code, etc.)
 
@@ -718,8 +718,7 @@ If none of these solutions work:
 
 ## Related Documentation
 
-- **[README.md](README.md)** - Core features and quick start
+- **[README.md](../README.md)** - Core features and quick start
 - **[ADVANCED.md](ADVANCED.md)** - Advanced features
 - **[FAQ.md](FAQ.md)** - Frequently asked questions
 - **[INSTALLING.md](INSTALLING.md)** - Installation guide
-- **[ADVANCED.md](ADVANCED.md)** - JSONL format and merge strategies
diff --git a/docs/adr/002-agent-mail-integration.md b/docs/adr/002-agent-mail-integration.md
index 2a35cecc..5f668122 100644
--- a/docs/adr/002-agent-mail-integration.md
+++ b/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
 
diff --git a/docs/dev-notes/ERROR_HANDLING_AUDIT.md b/docs/dev-notes/ERROR_HANDLING_AUDIT.md
index cb075cb3..426ffc8c 100644
--- a/docs/dev-notes/ERROR_HANDLING_AUDIT.md
+++ b/docs/dev-notes/ERROR_HANDLING_AUDIT.md
@@ -3,7 +3,7 @@
 **Issue:** bd-1qwo
 **Scope:** cmd/bd/*.go
 
-This document audits error handling patterns across the beads CLI codebase to ensure consistency with the guidelines established in [ERROR_HANDLING.md](ERROR_HANDLING.md).
+This document audits error handling patterns across the beads CLI codebase to ensure consistency with the guidelines established in [ERROR_HANDLING.md](../ERROR_HANDLING.md).
 
 ## Executive Summary