feat: Add bd repos multi-repo commands and fix bd ready for in_progress issues

- Add 'bd repos' command for multi-repository management (bd-123)
  - bd repos list: show all cached repositories
  - bd repos ready: aggregate ready work across repos
  - bd repos stats: combined statistics across repos
  - bd repos clear-cache: clear repository cache
  - Requires global daemon (bd daemon --global)

- Fix bd ready to show in_progress issues (bd-165)
  - bd ready now shows both 'open' and 'in_progress' issues with no blockers
  - Allows epics/tasks ready to close to appear in ready work
  - Critical P0 bug fix for workflow

- Apply code review improvements to repos implementation
  - Use strongly typed RPC responses (remove interface{})
  - Fix clear-cache lock handling (close connections outside lock)
  - Add error collection for per-repo failures
  - Add context timeouts (1-2s) to prevent hangs
  - Add lock strategy comments

- Update documentation (README.md, AGENTS.md)
- Add comprehensive tests for both features

Amp-Thread-ID: https://ampcode.com/threads/T-1de989a1-1890-492c-9847-a34144259e0f
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/ready.go

@@ -10,18 +10,20 @@ import (
 )
 
 // GetReadyWork returns issues with no open blockers
+// By default, shows both 'open' and 'in_progress' issues so epics/tasks
+// ready to close are visible (bd-165)
 func (s *SQLiteStorage) GetReadyWork(ctx context.Context, filter types.WorkFilter) ([]*types.Issue, error) {
 	whereClauses := []string{}
 	args := []interface{}{}
 
-	// Default to open status if not specified
+	// Default to open OR in_progress if not specified (bd-165)
 	if filter.Status == "" {
-		filter.Status = types.StatusOpen
+		whereClauses = append(whereClauses, "i.status IN ('open', 'in_progress')")
+	} else {
+		whereClauses = append(whereClauses, "i.status = ?")
+		args = append(args, filter.Status)
 	}
 
-	whereClauses = append(whereClauses, "i.status = ?")
-	args = append(args, filter.Status)
-
 	if filter.Priority != nil {
 		whereClauses = append(whereClauses, "i.priority = ?")
 		args = append(args, *filter.Priority)

internal/storage/sqlite/ready_test.go

@@ -751,3 +751,74 @@ func TestDeepHierarchyBlocking(t *testing.T) {
 		}
 	}
 }
+
+func TestGetReadyWorkIncludesInProgress(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create issues:
+	// bd-1: open, no dependencies → READY
+	// bd-2: in_progress, no dependencies → READY (bd-165)
+	// bd-3: in_progress, depends on open issue → BLOCKED
+	// bd-4: closed, no dependencies → NOT READY (closed)
+
+	issue1 := &types.Issue{Title: "Open Ready", Status: types.StatusOpen, Priority: 1, IssueType: types.TypeTask}
+	issue2 := &types.Issue{Title: "In Progress Ready", Status: types.StatusInProgress, Priority: 2, IssueType: types.TypeEpic}
+	issue3 := &types.Issue{Title: "In Progress Blocked", Status: types.StatusInProgress, Priority: 1, IssueType: types.TypeTask}
+	issue4 := &types.Issue{Title: "Blocker", Status: types.StatusOpen, Priority: 1, IssueType: types.TypeTask}
+	issue5 := &types.Issue{Title: "Closed", Status: types.StatusClosed, Priority: 1, IssueType: types.TypeTask}
+
+	store.CreateIssue(ctx, issue1, "test-user")
+	store.CreateIssue(ctx, issue2, "test-user")
+	store.UpdateIssue(ctx, issue2.ID, map[string]interface{}{"status": types.StatusInProgress}, "test-user")
+	store.CreateIssue(ctx, issue3, "test-user")
+	store.UpdateIssue(ctx, issue3.ID, map[string]interface{}{"status": types.StatusInProgress}, "test-user")
+	store.CreateIssue(ctx, issue4, "test-user")
+	store.CreateIssue(ctx, issue5, "test-user")
+	store.CloseIssue(ctx, issue5.ID, "Done", "test-user")
+
+	// Add dependency: issue3 blocks on issue4
+	store.AddDependency(ctx, &types.Dependency{IssueID: issue3.ID, DependsOnID: issue4.ID, Type: types.DepBlocks}, "test-user")
+
+	// Get ready work (default filter - no status specified)
+	ready, err := store.GetReadyWork(ctx, types.WorkFilter{})
+	if err != nil {
+		t.Fatalf("GetReadyWork failed: %v", err)
+	}
+
+	// Should have 3 ready issues:
+	// - issue1 (open, no blockers)
+	// - issue2 (in_progress, no blockers) ← this is the key test case for bd-165
+	// - issue4 (open blocker, but itself has no blockers so it's ready to work on)
+	if len(ready) != 3 {
+		t.Logf("Ready issues:")
+		for _, r := range ready {
+			t.Logf("  - %s: %s (status: %s)", r.ID, r.Title, r.Status)
+		}
+		t.Fatalf("Expected 3 ready issues, got %d", len(ready))
+	}
+
+	// Verify ready issues
+	readyIDs := make(map[string]bool)
+	for _, issue := range ready {
+		readyIDs[issue.ID] = true
+	}
+
+	if !readyIDs[issue1.ID] {
+		t.Errorf("Expected %s (open, no blockers) to be ready", issue1.ID)
+	}
+	if !readyIDs[issue2.ID] {
+		t.Errorf("Expected %s (in_progress, no blockers) to be ready - this is bd-165!", issue2.ID)
+	}
+	if !readyIDs[issue4.ID] {
+		t.Errorf("Expected %s (open blocker, but itself unblocked) to be ready", issue4.ID)
+	}
+	if readyIDs[issue3.ID] {
+		t.Errorf("Expected %s (in_progress, blocked) to NOT be ready", issue3.ID)
+	}
+	if readyIDs[issue5.ID] {
+		t.Errorf("Expected %s (closed) to NOT be ready", issue5.ID)
+	}
+}