fix(doctor): detect plugin and hooks in project-level settings (#1091)

* fix(doctor): detect beads plugin in project-level settings

isBeadsPluginInstalled() now checks project-level settings files
(.claude/settings.json and .claude/settings.local.json) in addition
to user-level settings (~/.claude/settings.json).

This fixes the contradictory bd doctor output where the plugin check
passes but the integration check warns "Not configured" when the
plugin is enabled at project scope.

Fixes #1090

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(doctor): detect Claude hooks in project-level settings.json

hasClaudeHooks() was missing .claude/settings.json - it only checked
.claude/settings.local.json for project-level hooks.

Now checks all three locations:
- ~/.claude/settings.json (user-level)
- .claude/settings.json (project-level)
- .claude/settings.local.json (project-level, gitignored)

Also uses filepath.Join consistently for cross-platform compatibility.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/doctor/claude.go

@@ -81,15 +81,39 @@ func CheckClaude() DoctorCheck {
 	}
 }
 
-// isBeadsPluginInstalled checks if beads plugin is enabled in Claude Code
+// isBeadsPluginInstalled checks if beads plugin is enabled in Claude Code.
+// It checks user-level (~/.claude/settings.json) and project-level settings
+// (.claude/settings.json and .claude/settings.local.json).
 func isBeadsPluginInstalled() bool {
 	home, err := os.UserHomeDir()
 	if err != nil {
 		return false
 	}
 
-	settingsPath := filepath.Join(home, ".claude/settings.json")
-	data, err := os.ReadFile(settingsPath) // #nosec G304 -- settingsPath is constructed from user home dir, not user input
+	// Check user-level settings
+	userSettings := filepath.Join(home, ".claude", "settings.json")
+	if checkPluginInSettings(userSettings) {
+		return true
+	}
+
+	// Check project-level settings
+	projectSettings := filepath.Join(".claude", "settings.json")
+	if checkPluginInSettings(projectSettings) {
+		return true
+	}
+
+	// Check project-level local settings (gitignored)
+	projectLocalSettings := filepath.Join(".claude", "settings.local.json")
+	if checkPluginInSettings(projectLocalSettings) {
+		return true
+	}
+
+	return false
+}
+
+// checkPluginInSettings checks if beads plugin is enabled in a settings file
+func checkPluginInSettings(settingsPath string) bool {
+	data, err := os.ReadFile(settingsPath) // #nosec G304 -- settingsPath is constructed from known safe locations, not user input
 	if err != nil {
 		return false
 	}
@@ -159,10 +183,11 @@ func hasClaudeHooks() bool {
 		return false
 	}
 
-	globalSettings := filepath.Join(home, ".claude/settings.json")
-	projectSettings := ".claude/settings.local.json"
+	globalSettings := filepath.Join(home, ".claude", "settings.json")
+	projectSettings := filepath.Join(".claude", "settings.json")
+	projectLocalSettings := filepath.Join(".claude", "settings.local.json")
 
-	return hasBeadsHooks(globalSettings) || hasBeadsHooks(projectSettings)
+	return hasBeadsHooks(globalSettings) || hasBeadsHooks(projectSettings) || hasBeadsHooks(projectLocalSettings)
 }
 
 // hasBeadsHooks checks if a settings file has bd prime hooks