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.go

@@ -65,11 +65,6 @@ func InstallClaude(project bool, stealth bool) {
 		fmt.Println("✓ Registered PreCompact hook")
 	}
 
-	// Add bd to allowedTools so commands don't require per-command approval
-	if addAllowedTool(settings, "Bash(bd *)") {
-		fmt.Println("✓ Added bd to allowedTools (no per-command approval needed)")
-	}
-
 	// Write back to file
 	data, err = json.MarshalIndent(settings, "", "  ")
 	if err != nil {
@@ -154,9 +149,6 @@ func RemoveClaude(project bool) {
 	removeHookCommand(hooks, "SessionStart", "bd prime --stealth")
 	removeHookCommand(hooks, "PreCompact", "bd prime --stealth")
 
-	// Remove bd from allowedTools
-	removeAllowedTool(settings, "Bash(bd *)")
-
 	// Write back
 	data, err = json.MarshalIndent(settings, "", "  ")
 	if err != nil {
@@ -172,49 +164,6 @@ func RemoveClaude(project bool) {
 	fmt.Println("✓ Claude hooks removed")
 }
 
-// addAllowedTool adds a tool pattern to allowedTools if not already present
-// Returns true if tool was added, false if already exists
-func addAllowedTool(settings map[string]interface{}, tool string) bool {
-	// Get or create allowedTools array
-	allowedTools, ok := settings["allowedTools"].([]interface{})
-	if !ok {
-		allowedTools = []interface{}{}
-	}
-
-	// Check if tool already in list
-	for _, t := range allowedTools {
-		if t == tool {
-			fmt.Printf("✓ Tool already in allowedTools: %s\n", tool)
-			return false
-		}
-	}
-
-	// Add tool to array
-	allowedTools = append(allowedTools, tool)
-	settings["allowedTools"] = allowedTools
-	return true
-}
-
-// removeAllowedTool removes a tool pattern from allowedTools
-func removeAllowedTool(settings map[string]interface{}, tool string) {
-	allowedTools, ok := settings["allowedTools"].([]interface{})
-	if !ok {
-		return
-	}
-
-	// Filter out the tool
-	var filtered []interface{}
-	for _, t := range allowedTools {
-		if t != tool {
-			filtered = append(filtered, t)
-		} else {
-			fmt.Printf("✓ Removed %s from allowedTools\n", tool)
-		}
-	}
-
-	settings["allowedTools"] = filtered
-}
-
 // addHookCommand adds a hook command to an event if not already present
 // Returns true if hook was added, false if already exists
 func addHookCommand(hooks map[string]interface{}, event, command string) bool {