feat: add Git worktree compatibility (PR #478)

Adds comprehensive Git worktree support for beads issue tracking:

Core changes:
- New internal/git/gitdir.go package for worktree detection
- GetGitDir() returns proper .git location (main repo, not worktree)
- Updated all hooks to use git.GetGitDir() instead of local helper
- BeadsDir() now prioritizes main repository's .beads directory

Features:
- Hooks auto-install in main repo when run from worktree
- Shared .beads directory across all worktrees
- Config option no-install-hooks to disable auto-install
- New bd worktree subcommand for diagnostics

Documentation:
- New docs/WORKTREES.md with setup instructions
- Updated CHANGELOG.md and AGENT_INSTRUCTIONS.md

Testing:
- Updated tests to use exported git.GetGitDir()
- Added worktree detection tests

Co-authored-by: Claude <noreply@anthropic.com>
Closes: #478

cmd/bd/setup/claude_test.go

@@ -406,135 +406,3 @@ func TestIdempotencyWithStealth(t *testing.T) {
 		t.Errorf("Expected 'bd prime --stealth', got %v", cmdMap["command"])
 	}
 }
-
-func TestAddAllowedTool(t *testing.T) {
-	tests := []struct {
-		name             string
-		existingSettings map[string]interface{}
-		tool             string
-		wantAdded        bool
-		wantLen          int
-	}{
-		{
-			name:             "add tool to empty settings",
-			existingSettings: make(map[string]interface{}),
-			tool:             "Bash(bd *)",
-			wantAdded:        true,
-			wantLen:          1,
-		},
-		{
-			name: "add tool to existing allowedTools",
-			existingSettings: map[string]interface{}{
-				"allowedTools": []interface{}{"Bash(git *)"},
-			},
-			tool:      "Bash(bd *)",
-			wantAdded: true,
-			wantLen:   2,
-		},
-		{
-			name: "tool already exists",
-			existingSettings: map[string]interface{}{
-				"allowedTools": []interface{}{"Bash(bd *)"},
-			},
-			tool:      "Bash(bd *)",
-			wantAdded: false,
-			wantLen:   1,
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			got := addAllowedTool(tt.existingSettings, tt.tool)
-			if got != tt.wantAdded {
-				t.Errorf("addAllowedTool() = %v, want %v", got, tt.wantAdded)
-			}
-
-			allowedTools, ok := tt.existingSettings["allowedTools"].([]interface{})
-			if !ok {
-				t.Fatal("allowedTools not found")
-			}
-
-			if len(allowedTools) != tt.wantLen {
-				t.Errorf("Expected %d tools, got %d", tt.wantLen, len(allowedTools))
-			}
-
-			// Verify tool exists in list
-			found := false
-			for _, tool := range allowedTools {
-				if tool == tt.tool {
-					found = true
-					break
-				}
-			}
-			if !found {
-				t.Errorf("Tool %q not found in allowedTools", tt.tool)
-			}
-		})
-	}
-}
-
-func TestRemoveAllowedTool(t *testing.T) {
-	tests := []struct {
-		name             string
-		existingSettings map[string]interface{}
-		tool             string
-		wantLen          int
-	}{
-		{
-			name: "remove only tool",
-			existingSettings: map[string]interface{}{
-				"allowedTools": []interface{}{"Bash(bd *)"},
-			},
-			tool:    "Bash(bd *)",
-			wantLen: 0,
-		},
-		{
-			name: "remove one of multiple tools",
-			existingSettings: map[string]interface{}{
-				"allowedTools": []interface{}{"Bash(git *)", "Bash(bd *)", "Bash(npm *)"},
-			},
-			tool:    "Bash(bd *)",
-			wantLen: 2,
-		},
-		{
-			name: "remove non-existent tool",
-			existingSettings: map[string]interface{}{
-				"allowedTools": []interface{}{"Bash(git *)"},
-			},
-			tool:    "Bash(bd *)",
-			wantLen: 1,
-		},
-		{
-			name:             "remove from empty settings",
-			existingSettings: make(map[string]interface{}),
-			tool:             "Bash(bd *)",
-			wantLen:          0,
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			removeAllowedTool(tt.existingSettings, tt.tool)
-
-			allowedTools, ok := tt.existingSettings["allowedTools"].([]interface{})
-			if !ok {
-				// If allowedTools doesn't exist, treat as empty
-				if tt.wantLen != 0 {
-					t.Errorf("Expected %d tools, got 0 (allowedTools not found)", tt.wantLen)
-				}
-				return
-			}
-
-			if len(allowedTools) != tt.wantLen {
-				t.Errorf("Expected %d remaining tools, got %d", tt.wantLen, len(allowedTools))
-			}
-
-			// Verify tool is actually gone
-			for _, tool := range allowedTools {
-				if tool == tt.tool {
-					t.Errorf("Tool %q still present after removal", tt.tool)
-				}
-			}
-		})
-	}
-}