feat: complete bd-kwro messaging & knowledge graph epic

- Add bd cleanup --ephemeral flag for transient message cleanup (bd-kwro.9)
- Add Ephemeral filter to IssueFilter type
- Add ephemeral filtering to SQLite storage queries

Tests (bd-kwro.10):
- Add internal/hooks/hooks_test.go for hook system
- Add cmd/bd/mail_test.go for mail commands
- Add internal/storage/sqlite/graph_links_test.go for graph links

Documentation (bd-kwro.11):
- Add docs/messaging.md for full messaging reference
- Add docs/graph-links.md for graph link types
- Update AGENTS.md with inter-agent messaging section
- Update CHANGELOG.md with all bd-kwro features

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

AGENTS.md

@@ -332,6 +332,47 @@ bd close bd-42 "Done"                       # Updates via git sync
 
 See [docs/AGENT_MAIL_QUICKSTART.md](docs/AGENT_MAIL_QUICKSTART.md) for 5-minute setup, or [docs/AGENT_MAIL.md](docs/AGENT_MAIL.md) for complete documentation. Example code in [examples/python-agent/AGENT_MAIL_EXAMPLE.md](examples/python-agent/AGENT_MAIL_EXAMPLE.md).
 
+### Inter-Agent Messaging (bd mail)
+
+Beads includes a built-in messaging system for direct agent-to-agent communication. Messages are stored as beads issues, synced via git.
+
+**Setup:**
+
+```bash
+# Set your identity (add to environment or .beads/config.json)
+export BEADS_IDENTITY="worker-1"
+```
+
+**Commands:**
+
+```bash
+# Send a message
+bd mail send <recipient> -s "Subject" -m "Body"
+bd mail send worker-2 -s "Handoff" -m "Your turn on bd-xyz" --urgent
+
+# Check your inbox
+bd mail inbox
+
+# Read a specific message
+bd mail read bd-a1b2
+
+# Acknowledge (mark as read/close)
+bd mail ack bd-a1b2
+
+# Reply to a message (creates thread)
+bd mail reply bd-a1b2 -m "Thanks, on it!"
+```
+
+**Use cases:**
+- Task handoffs between agents
+- Status updates to coordinator
+- Blocking questions requiring response
+- Priority signaling with `--urgent` flag
+
+**Cleanup:** Messages are ephemeral. Run `bd cleanup --ephemeral --force` to delete closed messages.
+
+See [docs/messaging.md](docs/messaging.md) for full documentation.
+
 ### Deletion Tracking
 
 When issues are deleted (via `bd delete` or `bd cleanup`), they are recorded in `.beads/deletions.jsonl`. This manifest:
@@ -378,10 +419,19 @@ bd deleted --json              # Machine-readable output
 
 ### Dependency Types
 
+**Blocking dependencies:**
 - `blocks` - Hard dependency (issue X blocks issue Y)
-- `related` - Soft relationship (issues are connected)
+
+**Structural relationships:**
 - `parent-child` - Epic/subtask relationship
 - `discovered-from` - Track issues discovered during work (automatically inherits parent's `source_repo`)
+- `related` - Soft relationship (issues are connected)
+
+**Graph links:** (see [docs/graph-links.md](docs/graph-links.md))
+- `relates_to` - Bidirectional "see also" links (`bd relate <id1> <id2>`)
+- `duplicates` - Mark issue as duplicate (`bd duplicate <id> --of <canonical>`)
+- `supersedes` - Version chains (`bd supersede <old> --with <new>`)
+- `replies_to` - Message threads (`bd mail reply`)
 
 Only `blocks` dependencies affect the ready work queue.