fix(security): expand default allowed_commands and auto_approve (#2486)

src/openhuman/config/schema/autonomy.rs

@@ -60,9 +60,18 @@ fn default_max_cost_per_day_cents() -> u32 {
 
 fn default_allowed_commands() -> Vec<String> {
     vec![
+        // Version control
         "git".into(),
+        // Package managers / build systems. `make` can run arbitrary recipes,
+        // but the shell policy still gates execution to this command allow-list
+        // and Supervised mode approval remains responsible for risky invocations.
         "npm".into(),
+        "pnpm".into(),
+        "yarn".into(),
         "cargo".into(),
+        "make".into(),
+        "cmake".into(),
+        // Directory / file inspection (read-only)
         "ls".into(),
         "cat".into(),
         "grep".into(),
@@ -73,6 +82,26 @@ fn default_allowed_commands() -> Vec<String> {
         "head".into(),
         "tail".into(),
         "date".into(),
+        "sort".into(),
+        "uniq".into(),
+        "diff".into(),
+        "which".into(),
+        "uname".into(),
+        "basename".into(),
+        "dirname".into(),
+        "tr".into(),
+        "cut".into(),
+        "realpath".into(),
+        "readlink".into(),
+        "stat".into(),
+        "file".into(),
+        // Filesystem mutations (medium-risk — require approval in Supervised mode)
+        "mkdir".into(),
+        "touch".into(),
+        "cp".into(),
+        "mv".into(),
+        "ln".into(),
+        // Windows read-only equivalents for ls/cat/grep/which
         "dir".into(),
         "type".into(),
         "where".into(),
@@ -106,11 +135,15 @@ fn default_forbidden_paths() -> Vec<String> {
 
 fn default_auto_approve() -> Vec<String> {
     vec![
+        // Read-only tools — always safe to skip the approval prompt
         "file_read".into(),
         "memory_search".into(),
         "memory_list".into(),
         "get_time".into(),
         "list_dir".into(),
+        // Workspace-scoped search tools — read-only, no side effects
+        "glob".into(),
+        "grep".into(),
     ]
 }