feat: implement --max-depth flag for bd dep tree (closes #87, bd-3, bd-159)

- Add --max-depth/-d flag with default of 50
- Wire flag through to store.GetDependencyTree()
- Add input validation (must be >= 1)
- Show inline '… [truncated]' markers on truncated nodes
- Update truncation warning to show actual depth used
- Add comprehensive tests (truncation, default depth, boundary cases)
- Update CLI docs and reference

Thanks to @yashwanth-reddy909 for the initial implementation in PR #87.
This commit completes the feature with full wiring, validation, tests, and docs.

Amp-Thread-ID: https://ampcode.com/threads/T-c439b09c-cff2-48d9-8988-cf9353f0d32e
Co-authored-by: Amp <amp@ampcode.com>

.beads/issues.jsonl

@@ -64,6 +64,7 @@
 {"id":"bd-156","title":"Refactor import logic to eliminate duplication between manual and auto-import","description":"The import logic is duplicated in two places:\n1. cmd/bd/import.go (manual 'bd import' command)\n2. cmd/bd/main.go:autoImportIfNewer() (auto-import after git pull)\n\nBoth have nearly identical code for:\n- Reading and parsing JSONL\n- Type-asserting store to *sqlite.SQLiteStorage (where we just fixed a bug twice)\n- Opening direct SQLite connection when using daemon mode\n- Detecting collisions with sqlite.DetectCollisions()\n- Scoring and remapping collisions\n- Importing issues, dependencies, and labels\n\n**Problems:**\n- Bugs must be fixed in two places (we just did this for daemon mode)\n- Features must be implemented twice\n- Tests must cover both code paths\n- Harder to maintain and keep in sync\n- Higher risk of divergence over time\n\n**Proposed solution:**\nExtract a shared function that handles the core import logic:\n\n```go\n// importIssues handles the core import logic used by both manual and auto-import\nfunc importIssues(ctx context.Context, dbPath string, store storage.Storage, \n                  issues []*types.Issue, opts ImportOptions) (*ImportResult, error) {\n    // Handle SQLite store detection/creation for daemon mode\n    // Detect collisions\n    // Score and remap if needed\n    // Import issues, dependencies, labels\n    // Return result\n}\n```\n\nBoth import.go and autoImportIfNewer() would call this shared function with their specific options.\n\n**Benefits:**\n- Single source of truth for import logic\n- Bugs fixed once\n- Easier to test\n- Easier to extend with new import features\n- Less code overall","status":"closed","priority":2,"issue_type":"chore","created_at":"2025-10-18T17:07:06.007026-07:00","updated_at":"2025-10-18T18:35:11.753484-07:00","closed_at":"2025-10-18T17:11:20.280214-07:00"}
 {"id":"bd-157","title":"Complete auto-import refactoring to use shared importIssuesCore function","description":"The manual import command (bd import) was successfully refactored to use the shared importIssuesCore() function in import_shared.go, reducing code from 494 lines to 170 lines.\n\nHowever, autoImportIfNewer() in cmd/bd/main.go still has ~298 lines of duplicated import logic that should use the same shared function.\n\n**Current state:**\n- ✅ Manual import uses importIssuesCore() (commit 790233f)\n- ❌ Auto-import still has duplicated logic (lines 618-915 in main.go)\n\n**Duplication includes:**\n- SQLite store detection/creation for daemon mode (fixed in 790233f)\n- Collision detection with sqlite.DetectCollisions()\n- Scoring and remapping collisions\n- Importing issues (update existing, create new)\n- Importing dependencies\n- Importing labels\n\n**Benefits of completing this:**\n- Remove ~200 more lines of duplicated code\n- Ensure manual and auto-import have identical behavior\n- Future bug fixes only need to be made once\n- Easier to test and maintain\n\n**Implementation:**\nReplace lines 714-908 in autoImportIfNewer() with:\n```go\nopts := ImportOptions{\n    ResolveCollisions: true,  // Auto-import always resolves\n    DryRun:            false,\n    SkipUpdate:        false,\n    Strict:            false,\n}\nresult, err := importIssuesCore(ctx, dbPath, store, allIssues, opts)\n// Handle result and show remapping notification\n```\n\nThen update hash storage logic at the end.","status":"closed","priority":2,"issue_type":"chore","created_at":"2025-10-18T17:38:34.443872-07:00","updated_at":"2025-10-18T18:35:11.754006-07:00","closed_at":"2025-10-18T18:07:05.553928-07:00"}
 {"id":"bd-158","title":"Add .gitignore to prevent noisy untracked beads files","description":"When using beads, git status shows several untracked files in .beads/ directory: .beads/.gitignore, .beads/db.sqlite, daemon.pid and daemon.lock files. These should be added to the project's .gitignore to prevent noise.","status":"open","priority":2,"issue_type":"chore","created_at":"2025-10-18T18:27:16.424878-07:00","updated_at":"2025-10-18T18:35:11.754574-07:00"}
+{"id":"bd-159","title":"Implement --max-depth flag for bd dep tree","description":"PR #87 adds the flag but doesn't wire it through. Need to:\n1. Add flag definition in cmd/bd/dep.go\n2. Pass maxDepth to store.GetDependencyTree()\n3. Fix truncation warning to show actual depth used\n4. Add tests for truncation behavior (TestGetDependencyTree_TruncationDepth, TestGetDependencyTree_DefaultDepth)\n5. Update CLI docs/help\n\nDefault should remain 50. Keep using direct storage mode (no RPC needed for now).\n\nRelated: PR #87, bd-3","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-10-19T08:31:15.473267-07:00","updated_at":"2025-10-19T08:55:21.266386-07:00","closed_at":"2025-10-19T08:55:21.266386-07:00"}
 {"id":"bd-16","title":"Add EXPLAIN QUERY PLAN tests for ready work query","description":"Verify that the hierarchical blocking query uses proper indexes and doesn't do full table scans.\n\n**Queries to analyze:**\n1. The recursive CTE (both base case and recursive case)\n2. The final SELECT with NOT EXISTS\n3. Impact of various filters (status, priority, assignee)\n\n**Implementation:**\nAdd test function that:\n- Runs EXPLAIN QUERY PLAN on GetReadyWork query\n- Parses output to verify no SCAN TABLE operations\n- Documents expected query plan in comments\n- Fails if query plan degrades\n\n**Benefits:**\n- Catch performance regressions in tests\n- Document expected query behavior\n- Ensure indexes are being used\n\nRelated to: bd-77 (composite index on depends_on_id, type)","status":"closed","priority":3,"issue_type":"task","created_at":"2025-10-16T20:46:08.971822-07:00","updated_at":"2025-10-18T18:35:11.755001-07:00","closed_at":"2025-10-18T12:47:44.284846-07:00"}
 {"id":"bd-17","title":"Make auto-flush debounce duration configurable","description":"flushDebounce is hardcoded to 5 seconds. Make it configurable via environment variable BEADS_FLUSH_DEBOUNCE (e.g., '500ms', '10s'). Current 5-second value is reasonable for interactive use, but CI/automated scenarios might want faster flush. Add getDebounceDuration() helper function. Located in cmd/bd/main.go:31.","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-10-16T20:46:08.971822-07:00","updated_at":"2025-10-18T18:35:11.755588-07:00","closed_at":"2025-10-18T09:47:43.22126-07:00"}
 {"id":"bd-18","title":"Optimize auto-flush to use incremental updates","description":"Every flush exports ALL issues and ALL dependencies, even if only one issue changed. For large projects (1000+ issues), this could be expensive. Current approach guarantees consistency, which is fine for MVP, but future optimization could track which issues changed and use incremental updates. Located in cmd/bd/main.go:255-276.","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-10-16T20:46:08.971822-07:00","updated_at":"2025-10-18T18:35:11.755965-07:00","closed_at":"2025-10-14T02:51:52.200141-07:00"}