fix: respect Claude CLI startup mode setting (#12)

The "Startup Mode" setting (normal/bypass/allowedTools) was saved to
settings but never read when spawning sessions. All code paths had
--dangerously-skip-permissions hardcoded. Now reads claudeMode from
~/.claudeman/settings.json and passes it through Session → TmuxManager.

Closes #12

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

CLAUDE.md

@@ -35,7 +35,7 @@ When user says "COM":
 1. Increment version in BOTH `package.json` AND `CLAUDE.md` (verify they match with `grep version package.json && grep Version CLAUDE.md`)
 2. Run: `git add -A && git commit -m "chore: bump version to X.XXXX" && git push && npm run build && systemctl --user restart claudeman-web`
 
-**Version**: 0.1617 (must match `package.json`)
+**Version**: 0.1618 (must match `package.json`)
 
 ## Project Overview
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "claudeman",
-  "version": "0.1617",
+  "version": "0.1618",
   "description": "The missing control plane for Claude Code - run 20 autonomous agents with real-time monitoring and session persistence",
   "type": "module",
   "main": "dist/index.js",

src/mux-interface.ts

@@ -7,7 +7,7 @@
  */
 
 import type { EventEmitter } from 'node:events';
-import type { ProcessStats, PersistedRespawnConfig, NiceConfig } from './types.js';
+import type { ProcessStats, PersistedRespawnConfig, NiceConfig, ClaudeMode } from './types.js';
 
 /**
  * Multiplexer session metadata.
@@ -71,6 +71,8 @@ export interface TerminalMultiplexer extends EventEmitter {
     name?: string,
     niceConfig?: NiceConfig,
     model?: string,
+    claudeMode?: ClaudeMode,
+    allowedTools?: string,
   ): Promise<MuxSession>;
 
   /**
@@ -163,5 +165,5 @@ export interface TerminalMultiplexer extends EventEmitter {
   isPaneDead(muxName: string): boolean;
 
   /** Respawn a dead pane with a fresh command. Returns the new PID or null on failure. */
-  respawnPane(sessionId: string, workingDir: string, mode: 'claude' | 'shell', niceConfig?: NiceConfig, model?: string): Promise<number | null>;
+  respawnPane(sessionId: string, workingDir: string, mode: 'claude' | 'shell', niceConfig?: NiceConfig, model?: string, claudeMode?: ClaudeMode, allowedTools?: string): Promise<number | null>;
 }

src/session.ts

@@ -18,7 +18,7 @@
 import { EventEmitter } from 'node:events';
 import { v4 as uuidv4 } from 'uuid';
 import * as pty from 'node-pty';
-import { SessionState, SessionStatus, SessionConfig, RalphTrackerState, RalphTodoItem, ActiveBashTool, NiceConfig, DEFAULT_NICE_CONFIG } from './types.js';
+import { SessionState, SessionStatus, SessionConfig, RalphTrackerState, RalphTodoItem, ActiveBashTool, NiceConfig, DEFAULT_NICE_CONFIG, type ClaudeMode } from './types.js';
 import type { TerminalMultiplexer, MuxSession } from './mux-interface.js';
 import { TaskTracker, type BackgroundTask } from './task-tracker.js';
 import { RalphTracker } from './ralph-tracker.js';
@@ -321,6 +321,10 @@ export class Session extends EventEmitter {
   // Claude model override (e.g., 'opus', 'sonnet', 'haiku')
   private _model: string | undefined;
 
+  // Claude CLI startup permission mode
+  private _claudeMode: ClaudeMode = 'dangerously-skip-permissions';
+  private _allowedTools: string | undefined;
+
   // Session color for visual differentiation
   private _color: import('./types.js').SessionColor = 'default';
 
@@ -374,6 +378,10 @@ export class Session extends EventEmitter {
     niceConfig?: NiceConfig;  // Nice prioritying configuration
     /** Claude model override (e.g., 'opus', 'sonnet', 'haiku') */
     model?: string;
+    /** Claude CLI startup permission mode */
+    claudeMode?: ClaudeMode;
+    /** Comma-separated allowed tools (for 'allowedTools' mode) */
+    allowedTools?: string;
   }) {
     super();
     this.setMaxListeners(25);
@@ -409,6 +417,14 @@ export class Session extends EventEmitter {
       this._model = config.model;
     }
 
+    // Apply Claude CLI permission mode
+    if (config.claudeMode) {
+      this._claudeMode = config.claudeMode;
+    }
+    if (config.allowedTools) {
+      this._allowedTools = config.allowedTools;
+    }
+
     // Initialize task tracker and forward events (store handlers for cleanup)
     this._taskTracker = new TaskTracker();
     this._taskTrackerHandlers = {
@@ -574,6 +590,36 @@ export class Session extends EventEmitter {
     return { ...this._niceConfig };
   }
 
+  /** Claude CLI startup permission mode */
+  get claudeMode(): ClaudeMode {
+    return this._claudeMode;
+  }
+
+  /** Allowed tools list (for 'allowedTools' mode) */
+  get allowedTools(): string | undefined {
+    return this._allowedTools;
+  }
+
+  /**
+   * Build Claude CLI permission flags based on the configured mode.
+   * Returns an array of args to pass to the CLI.
+   */
+  private _buildPermissionArgs(): string[] {
+    switch (this._claudeMode) {
+      case 'dangerously-skip-permissions':
+        return ['--dangerously-skip-permissions'];
+      case 'allowedTools':
+        if (this._allowedTools) {
+          return ['--allowedTools', this._allowedTools];
+        }
+        // Fall back to normal mode if no tools specified
+        return [];
+      case 'normal':
+      default:
+        return [];
+    }
+  }
+
   /**
    * Set CPU priority configuration.
    * Note: This only affects new sessions; existing running processes won't be changed.
@@ -829,9 +875,9 @@ export class Session extends EventEmitter {
   /**
    * Starts an interactive Claude CLI session with full terminal support.
    *
-   * This spawns Claude CLI with `--dangerously-skip-permissions` flag in
-   * interactive mode. If mux wrapping is enabled, the session runs inside
-   * a tmux session for persistence across disconnects.
+   * This spawns Claude CLI in interactive mode with the configured permission
+   * mode (default: `--dangerously-skip-permissions`). If mux wrapping is enabled,
+   * the session runs inside a tmux session for persistence across disconnects.
    *
    * @throws {Error} If a process is already running in this session
    *
@@ -872,7 +918,7 @@ export class Session extends EventEmitter {
         let needsNewSession = false;
         if (this._muxSession && this._mux.isPaneDead(this._muxSession.muxName)) {
           console.log('[Session] Dead pane detected, respawning:', this._muxSession.muxName);
-          const newPid = await this._mux.respawnPane(this.id, this.workingDir, 'claude', this._niceConfig, this._model);
+          const newPid = await this._mux.respawnPane(this.id, this.workingDir, 'claude', this._niceConfig, this._model, this._claudeMode, this._allowedTools);
           if (!newPid) {
             console.error('[Session] Failed to respawn pane, will create new session');
             needsNewSession = true;
@@ -888,7 +934,7 @@ export class Session extends EventEmitter {
           console.log('[Session] Attaching to existing mux session:', this._muxSession!.muxName);
         } else {
           // Create a new mux session
-          this._muxSession = await this._mux.createSession(this.id, this.workingDir, 'claude', this._name, this._niceConfig, this._model);
+          this._muxSession = await this._mux.createSession(this.id, this.workingDir, 'claude', this._name, this._niceConfig, this._model, this._claudeMode, this._allowedTools);
           console.log('[Session] Created mux session:', this._muxSession.muxName);
           // No extra sleep — createSession() already waits for tmux readiness
         }
@@ -961,7 +1007,7 @@ export class Session extends EventEmitter {
       try {
         // Pass --session-id to use the SAME ID as the Claudeman session
         // This ensures subagents can be directly matched to the correct tab
-        const args = ['--dangerously-skip-permissions', '--session-id', this.id];
+        const args = [...this._buildPermissionArgs(), '--session-id', this.id];
         if (this._model) args.push('--model', this._model);
         this.ptyProcess = pty.spawn('claude', args, {
           name: 'xterm-256color',

src/tmux-manager.ts

@@ -30,7 +30,7 @@ import { existsSync, readFileSync, mkdirSync } from 'node:fs';
 import { writeFile, rename } from 'node:fs/promises';
 import { dirname, join } from 'node:path';
 import { homedir } from 'node:os';
-import { ProcessStats, PersistedRespawnConfig, getErrorMessage, NiceConfig, DEFAULT_NICE_CONFIG, type PaneInfo } from './types.js';
+import { ProcessStats, PersistedRespawnConfig, getErrorMessage, NiceConfig, DEFAULT_NICE_CONFIG, type PaneInfo, type ClaudeMode } from './types.js';
 import { wrapWithNice } from './utils/nice-wrapper.js';
 import { SAFE_PATH_PATTERN } from './utils/regex-patterns.js';
 import type { TerminalMultiplexer, MuxSession, MuxSessionWithStats } from './mux-interface.js';
@@ -111,6 +111,31 @@ function isValidPath(path: string): boolean {
   return SAFE_PATH_PATTERN.test(path);
 }
 
+/**
+ * Build Claude CLI permission flags for the tmux command string.
+ * Validates allowedTools to prevent command injection.
+ */
+function buildClaudePermissionFlags(claudeMode?: ClaudeMode, allowedTools?: string): string {
+  const mode = claudeMode || 'dangerously-skip-permissions';
+  switch (mode) {
+    case 'dangerously-skip-permissions':
+      return ' --dangerously-skip-permissions';
+    case 'allowedTools':
+      if (allowedTools) {
+        // Sanitize: allow tool names with patterns like Bash(git:*), space/comma-separated
+        // Block shell metacharacters: ; & | $ ` \ { } < > ' " newlines
+        const hasDangerousChars = /[;&|$`\\{}<>'"[\]\n\r]/.test(allowedTools);
+        if (!hasDangerousChars) {
+          return ` --allowedTools "${allowedTools}"`;
+        }
+      }
+      // Fall back to normal mode if tools are invalid or missing
+      return '';
+    case 'normal':
+      return '';
+  }
+}
+
 /**
  * Manages tmux sessions that wrap Claude CLI or shell processes.
  *
@@ -204,6 +229,8 @@ export class TmuxManager extends EventEmitter implements TerminalMultiplexer {
     name?: string,
     niceConfig?: NiceConfig,
     model?: string,
+    claudeMode?: ClaudeMode,
+    allowedTools?: string,
   ): Promise<MuxSession> {
     const muxName = `claudeman-${sessionId.slice(0, 8)}`;
 
@@ -250,7 +277,7 @@ export class TmuxManager extends EventEmitter implements TerminalMultiplexer {
     const safeModel = (model && /^[a-zA-Z0-9._-]+$/.test(model)) ? model : undefined;
     const modelFlag = (mode === 'claude' && safeModel) ? ` --model ${safeModel}` : '';
     const baseCmd = mode === 'claude'
-      ? `claude --dangerously-skip-permissions --session-id "${sessionId}"${modelFlag}`
+      ? `claude${buildClaudePermissionFlags(claudeMode, allowedTools)} --session-id "${sessionId}"${modelFlag}`
       : '$SHELL';
 
     const config = niceConfig || DEFAULT_NICE_CONFIG;
@@ -394,7 +421,7 @@ export class TmuxManager extends EventEmitter implements TerminalMultiplexer {
    * Uses `tmux respawn-pane -k` to restart the command in the same pane,
    * preserving the session and its scrollback buffer.
    */
-  async respawnPane(sessionId: string, workingDir: string, mode: 'claude' | 'shell', niceConfig?: NiceConfig, model?: string): Promise<number | null> {
+  async respawnPane(sessionId: string, workingDir: string, mode: 'claude' | 'shell', niceConfig?: NiceConfig, model?: string, claudeMode?: ClaudeMode, allowedTools?: string): Promise<number | null> {
     const session = this.sessions.get(sessionId);
     if (!session) return null;
     const muxName = session.muxName;
@@ -415,7 +442,7 @@ export class TmuxManager extends EventEmitter implements TerminalMultiplexer {
     const safeModel = (model && /^[a-zA-Z0-9._-]+$/.test(model)) ? model : undefined;
     const modelFlag = (mode === 'claude' && safeModel) ? ` --model ${safeModel}` : '';
     const baseCmd = mode === 'claude'
-      ? `claude --dangerously-skip-permissions --session-id "${sessionId}"${modelFlag}`
+      ? `claude${buildClaudePermissionFlags(claudeMode, allowedTools)} --session-id "${sessionId}"${modelFlag}`
       : '$SHELL';
 
     const config = niceConfig || DEFAULT_NICE_CONFIG;

src/types.ts

@@ -105,6 +105,14 @@ export interface LifecycleEntry {
 
 // ========== Session Types ==========
 
+/**
+ * Claude CLI startup permission mode.
+ * - `'dangerously-skip-permissions'`: Bypass all permission prompts (default)
+ * - `'normal'`: Standard mode with permission prompts
+ * - `'allowedTools'`: Only allow specific tools (requires allowedTools list)
+ */
+export type ClaudeMode = 'dangerously-skip-permissions' | 'normal' | 'allowedTools';
+
 /**
  * Configuration for creating a new session
  */

src/web/server.ts

@@ -21,6 +21,7 @@ import { execSync } from 'node:child_process';
 import { homedir, totalmem, freemem, loadavg, cpus } from 'node:os';
 import { EventEmitter } from 'node:events';
 import { Session, ClaudeMessage, type BackgroundTask, type RalphTrackerState, type RalphTodoItem, type ActiveBashTool } from '../session.js';
+import type { ClaudeMode } from '../types.js';
 import { fileStreamManager } from '../file-stream-manager.js';
 import { RespawnController, RespawnConfig, RespawnState } from '../respawn-controller.js';
 import type { TerminalMultiplexer } from '../mux-interface.js';
@@ -839,6 +840,7 @@ export class WebServer extends EventEmitter {
       const globalNice = await this.getGlobalNiceConfig();
       const modelConfig = await this.getModelConfig();
       const model = (body.mode !== 'shell') ? modelConfig?.defaultModel : undefined;
+      const claudeModeConfig = await this.getClaudeModeConfig();
       const session = new Session({
         workingDir,
         mode: body.mode || 'claude',
@@ -847,6 +849,8 @@ export class WebServer extends EventEmitter {
         useMux: true,
         niceConfig: globalNice,
         model,
+        claudeMode: claudeModeConfig.claudeMode,
+        allowedTools: claudeModeConfig.allowedTools,
       });
 
       this.sessions.set(session.id, session);
@@ -2631,6 +2635,7 @@ export class WebServer extends EventEmitter {
       const niceConfig = await this.getGlobalNiceConfig();
       const qsModelConfig = await this.getModelConfig();
       const qsModel = (mode !== 'shell') ? qsModelConfig?.defaultModel : undefined;
+      const qsClaudeModeConfig = await this.getClaudeModeConfig();
       const session = new Session({
         workingDir: casePath,
         mux: this.mux,
@@ -2638,6 +2643,8 @@ export class WebServer extends EventEmitter {
         mode: mode,
         niceConfig: niceConfig,
         model: qsModel,
+        claudeMode: qsClaudeModeConfig.claudeMode,
+        allowedTools: qsClaudeModeConfig.allowedTools,
       });
 
       // Auto-detect completion phrase from CLAUDE.md BEFORE broadcasting
@@ -4681,6 +4688,18 @@ NOW: Generate the implementation plan for the task above. Think step by step.`;
     return undefined;
   }
 
+  // Helper to get Claude CLI startup mode from settings
+  private async getClaudeModeConfig(): Promise<{ claudeMode?: ClaudeMode; allowedTools?: string }> {
+    const settings = await this.readSettings();
+    const claudeMode = settings.claudeMode as string | undefined;
+    const allowedTools = settings.allowedTools as string | undefined;
+    // Only return valid modes
+    if (claudeMode === 'dangerously-skip-permissions' || claudeMode === 'normal' || claudeMode === 'allowedTools') {
+      return { claudeMode, allowedTools };
+    }
+    return {};
+  }
+
   // Helper to get model configuration from settings
   private async getModelConfig(): Promise<{ defaultModel?: string; agentTypeOverrides?: Record<string, string> } | null> {
     const settings = await this.readSettings();
@@ -5309,6 +5328,7 @@ NOW: Generate the implementation plan for the task above. Think step by step.`;
             const sessionName = savedState?.name || muxSession.name || muxSession.muxName;
 
             // Create a session object for this mux session
+            const recoveryClaudeMode = await this.getClaudeModeConfig();
             const session = new Session({
               id: muxSession.sessionId,  // Preserve the original session ID
               workingDir: muxSession.workingDir,
@@ -5316,7 +5336,9 @@ NOW: Generate the implementation plan for the task above. Think step by step.`;
               name: sessionName,
               mux: this.mux,
               useMux: true,
-              muxSession: muxSession  // Pass the existing session so startInteractive() can attach to it
+              muxSession: muxSession,  // Pass the existing session so startInteractive() can attach to it
+              claudeMode: recoveryClaudeMode.claudeMode,
+              allowedTools: recoveryClaudeMode.allowedTools,
             });
 
             // Update session name if it was a "Restored:" placeholder or doesn't match saved name