docs: Document multi-repo workflow with global daemon

Implements bd-122: Document how to use beads across multiple projects

Added comprehensive multi-repo documentation:
- README.md: Global daemon section with architecture diagram
- AGENTS.md: MCP multi-repo configuration (global daemon + per-project)
- integrations/beads-mcp/README.md: BEADS_WORKING_DIR usage
- Mermaid diagram showing one daemon serving multiple repos

Documentation covers:
- Global daemon (bd daemon --global) for system-wide usage
- Per-project MCP instances with BEADS_WORKING_DIR
- Comparison table (local vs global)
- When to use each approach
- Example workflows for multi-project setups

Benefits of global daemon:
- One daemon process for all repos
- Automatic socket discovery (local -> global fallback)
- Better resource usage
- Per-request context routing to correct database

Amp-Thread-ID: https://ampcode.com/threads/T-ea606216-b886-4af0-bba8-56d000362d01
Co-authored-by: Amp <amp@ampcode.com>

.beads/issues.jsonl

@@ -23,7 +23,7 @@
 {"id":"bd-119","title":"Issue in repo1","description":"This should go to repo1 database","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-17T16:35:02.535742-07:00","updated_at":"2025-10-17T18:13:19.394276-07:00","closed_at":"2025-10-17T18:13:19.394276-07:00"}
 {"id":"bd-12","title":"Implement reference scoring algorithm","description":"Count references for each colliding issue: text mentions in descriptions/notes/design fields + dependency references. Sort collisions by score ascending (fewest refs first). This minimizes total updates during renumbering.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-16T20:46:08.971822-07:00","updated_at":"2025-10-17T01:32:00.634423-07:00","closed_at":"2025-10-14T02:51:52.198288-07:00","dependencies":[{"issue_id":"bd-12","depends_on_id":"bd-48","type":"parent-child","created_at":"2025-10-16T21:51:08.913972-07:00","created_by":"renumber"}]}
 {"id":"bd-120","title":"Fix nil pointer crash in bd export command","description":"When running `bd export -o .beads/issues.jsonl`, the command crashes with a nil pointer dereference.\n\n## Error\n```\npanic: runtime error: invalid memory address or nil pointer dereference\n[signal SIGSEGV: segmentation violation code=0x2 addr=0x108 pc=0x1034456fc]\n\ngoroutine 1 [running]:\nmain.init.func14(0x103c24380, {0x1034a9695?, 0x4?, 0x1034a95c9?})\n        /Users/stevey/src/vc/adar/beads/cmd/bd/export.go:74 +0x15c\n```\n\n## Context\n- This happened after closing bd-105, bd-114, bd-115\n- Auto-export from daemon still works fine\n- Only the manual `bd export` command crashes\n- Data was already synced via auto-export, so no data loss\n\n## Location\nFile: `cmd/bd/export.go` line 74","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-17T17:34:05.014619-07:00","updated_at":"2025-10-17T17:35:41.414218-07:00","closed_at":"2025-10-17T17:35:41.414218-07:00"}
-{"id":"bd-121","title":"Add --global flag to daemon for multi-repo support","description":"Currently daemon creates socket at .beads/bd.sock in each repo. For multi-repo support, add --global flag to create socket in ~/.beads/bd.sock that can serve requests from any repository.\n\nImplementation:\n- Add --global flag to daemon command\n- When --global is set, use ~/.beads/bd.sock instead of ./.beads/bd.sock  \n- Don't require being in a git repo when --global is used\n- Update daemon discovery logic to check ~/.beads/bd.sock as fallback\n- Document that global daemon can serve multiple repos simultaneously\n\nBenefits:\n- Single daemon serves all repos on the system\n- No need to start daemon per-repo\n- Better resource usage\n- Enables system-wide task tracking\n\nContext: Per-request context routing (bd-115) already implemented - daemon can handle multiple repos. This issue is about making the UX better.\n\nRelated: bd-73 (parent issue for multi-repo support)","status":"open","priority":1,"issue_type":"feature","created_at":"2025-10-17T20:43:47.080685-07:00","updated_at":"2025-10-17T20:43:47.080685-07:00","dependencies":[{"issue_id":"bd-121","depends_on_id":"bd-73","type":"parent-child","created_at":"2025-10-17T20:44:02.2335-07:00","created_by":"daemon"}]}
+{"id":"bd-121","title":"Add --global flag to daemon for multi-repo support","description":"Currently daemon creates socket at .beads/bd.sock in each repo. For multi-repo support, add --global flag to create socket in ~/.beads/bd.sock that can serve requests from any repository.\n\nImplementation:\n- Add --global flag to daemon command\n- When --global is set, use ~/.beads/bd.sock instead of ./.beads/bd.sock  \n- Don't require being in a git repo when --global is used\n- Update daemon discovery logic to check ~/.beads/bd.sock as fallback\n- Document that global daemon can serve multiple repos simultaneously\n\nBenefits:\n- Single daemon serves all repos on the system\n- No need to start daemon per-repo\n- Better resource usage\n- Enables system-wide task tracking\n\nContext: Per-request context routing (bd-115) already implemented - daemon can handle multiple repos. This issue is about making the UX better.\n\nRelated: bd-73 (parent issue for multi-repo support)","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-10-17T20:43:47.080685-07:00","updated_at":"2025-10-17T22:45:42.411986-07:00","closed_at":"2025-10-17T22:45:42.411986-07:00","dependencies":[{"issue_id":"bd-121","depends_on_id":"bd-73","type":"parent-child","created_at":"2025-10-17T20:44:02.2335-07:00","created_by":"daemon"}]}
 {"id":"bd-122","title":"Document multi-repo workflow with daemon","description":"The daemon already supports multi-repo via per-request context routing (bd-115), but this isn't documented. Users need to know how to use beads across multiple projects.\n\nAdd documentation for:\n1. How daemon serves multiple repos simultaneously\n2. Starting daemon in one repo, using from others\n3. MCP server multi-repo configuration\n4. Example: tracking work across a dozen projects\n5. Comparison to workspace/global instance approaches\n\nDocumentation locations:\n- README.md (Multi-repo section)\n- AGENTS.md (MCP multi-repo config)\n- integrations/beads-mcp/README.md (working_dir parameter)\n\nInclude:\n- Architecture diagram showing one daemon, many repos\n- Example MCP config with BEADS_WORKING_DIR\n- CLI workflow example\n- Reference to test_multi_repo.py as proof of concept\n\nContext: Feature already works (proven by test_multi_repo.py), just needs user-facing docs.","status":"open","priority":1,"issue_type":"task","created_at":"2025-10-17T20:43:48.91315-07:00","updated_at":"2025-10-17T20:43:48.91315-07:00","dependencies":[{"issue_id":"bd-122","depends_on_id":"bd-73","type":"parent-child","created_at":"2025-10-17T20:44:03.261924-07:00","created_by":"daemon"}]}
 {"id":"bd-123","title":"Add 'bd repos' command for multi-repo aggregation","description":"When using daemon in multi-repo mode, users need commands to view/manage work across all active repositories.\n\nAdd 'bd repos' subcommand with:\n\n1. bd repos list\n   - Show all repositories daemon has cached\n   - Display: path, prefix, issue count, last activity\n   - Example output:\n     ~/src/project1  [p1-]   45 issues  (active)\n     ~/src/project2  [p2-]   12 issues  (2m ago)\n\n2. bd repos ready --all  \n   - Aggregate ready work across all repos\n   - Group by repo or show combined list\n   - Support priority/assignee filters\n\n3. bd repos stats\n   - Combined statistics across all repos\n   - Total issues, breakdown by status/priority\n   - Per-repo breakdown\n\n4. bd repos clear-cache\n   - Close all cached storage connections\n   - Useful for freeing resources\n\nImplementation notes:\n- Requires daemon to track active storage instances\n- May need RPC protocol additions for multi-repo queries\n- Should gracefully handle repos that no longer exist\n\nDepends on: Global daemon flag (makes this more useful)\n\nContext: This provides the UX layer on top of existing multi-repo support. The daemon can already serve multiple repos - this makes it easy to work with them.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-10-17T20:43:49.816998-07:00","updated_at":"2025-10-17T20:43:49.816998-07:00","dependencies":[{"issue_id":"bd-123","depends_on_id":"bd-73","type":"parent-child","created_at":"2025-10-17T20:44:04.407138-07:00","created_by":"daemon"},{"issue_id":"bd-123","depends_on_id":"bd-121","type":"blocks","created_at":"2025-10-17T20:44:13.681626-07:00","created_by":"daemon"}]}
 {"id":"bd-124","title":"Add daemon auto-start on first use","description":"Currently users must manually start daemon with 'bd daemon'. For better UX, auto-start daemon when first bd command is run.\n\nImplementation:\n\n1. In PersistentPreRun, check if daemon is running\n2. If not, check if auto-start is enabled (default: true)\n3. Start daemon with appropriate flags (--global if configured)\n4. Wait for socket to be ready (with timeout)\n5. Retry connection to newly-started daemon\n6. Silently fail back to direct mode if daemon won't start\n\nConfiguration:\n- BEADS_AUTO_START_DAEMON env var (default: true)\n- --no-auto-daemon flag to disable\n- Config file option: auto_start_daemon = true\n\nSafety considerations:\n- Don't auto-start if daemon failed recently (exponential backoff)\n- Log auto-start to daemon.log\n- Clear error messages if auto-start fails\n- Never auto-start if --no-daemon flag is set\n\nBenefits:\n- Zero-configuration experience\n- Daemon benefits (speed, multi-repo) automatic\n- Still supports direct mode as fallback\n\nDepends on: Global daemon flag would make this more useful","status":"open","priority":2,"issue_type":"feature","created_at":"2025-10-17T20:43:50.961453-07:00","updated_at":"2025-10-17T20:43:50.961453-07:00","dependencies":[{"issue_id":"bd-124","depends_on_id":"bd-73","type":"parent-child","created_at":"2025-10-17T20:44:05.502634-07:00","created_by":"daemon"},{"issue_id":"bd-124","depends_on_id":"bd-121","type":"blocks","created_at":"2025-10-17T20:44:14.987308-07:00","created_by":"daemon"}]}