feat(permissions): implement permission system with plan mode enforcement (M1 complete)

This commit implements the complete M1 milestone (Config & Permissions) including:

- New permissions crate with Tool, Action, Mode, and PermissionManager
- Three permission modes: Plan (read-only default), AcceptEdits, Code
- Pattern matching for permission rules (exact match and prefix with *)
- Integration with config-agent for mode-based permission management
- CLI integration with --mode flag to override configured mode
- Permission checks for Read, Glob, and Grep operations
- Comprehensive test suite (10 tests in permissions, 4 in config, 4 in CLI)

Also fixes:
- Fixed failing test in tools-fs (glob pattern issue)
- Improved glob_list() root extraction to handle patterns like "/*.txt"

All 21 workspace tests passing.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

crates/platform/config/tests/precedence.rs

@@ -1,4 +1,5 @@
 use config_agent::{load_settings, Settings};
+use permissions::{Mode, PermissionDecision, Tool};
 use std::{env, fs};
 
 #[test]
@@ -16,4 +17,32 @@ fn precedence_env_overrides_files() {
 fn default_mode_is_plan() {
     let s = Settings::default();
     assert_eq!(s.mode, "plan");
+}
+
+#[test]
+fn settings_create_permission_manager_with_plan_mode() {
+    let s = Settings::default();
+    let mgr = s.create_permission_manager();
+
+    // Plan mode should allow read operations
+    assert_eq!(mgr.check(Tool::Read, None), PermissionDecision::Allow);
+
+    // Plan mode should ask for write operations
+    assert_eq!(mgr.check(Tool::Write, None), PermissionDecision::Ask);
+}
+
+#[test]
+fn settings_parse_mode_from_config() {
+    let tmp = tempfile::tempdir().unwrap();
+    let project_file = tmp.path().join(".owlen.toml");
+    fs::write(&project_file, r#"mode="code""#).unwrap();
+
+    let s = load_settings(Some(tmp.path().to_str().unwrap())).unwrap();
+    assert_eq!(s.mode, "code");
+    assert_eq!(s.get_mode(), Mode::Code);
+
+    let mgr = s.create_permission_manager();
+    // Code mode should allow everything
+    assert_eq!(mgr.check(Tool::Write, None), PermissionDecision::Allow);
+    assert_eq!(mgr.check(Tool::Bash, None), PermissionDecision::Allow);
 }