fix(cli): include initial connection time in command duration

Fixes bounty issue #1521

The `cortex run` command was starting the timer after the initial connection
and submission were completed, which resulted in underreported duration for
commands, especially when connection setup was slow.

This change moves the timer start to before the submission is sent, ensuring
that the reported duration includes the full end-to-end time.

Author: factorydroid

cortex-cli/src/run_cmd.rs

@@ -510,6 +510,16 @@ impl RunCli {
             input_parts
         };
 
+        // Set up timeout if specified
+        let timeout_duration = if self.timeout > 0 {
+            Some(Duration::from_secs(self.timeout))
+        } else {
+            None
+        };
+
+        // Start timing before submission to include connection time
+        let start_time = std::time::Instant::now();
+
         // Send the submission
         let submission = Submission {
             id: uuid::Uuid::new_v4().to_string(),
@@ -523,15 +533,6 @@ impl RunCli {
         let mut streaming_started = false;
         let mut error_occurred = false;
 
-        // Set up timeout if specified
-        let timeout_duration = if self.timeout > 0 {
-            Some(Duration::from_secs(self.timeout))
-        } else {
-            None
-        };
-
-        let start_time = std::time::Instant::now();
-
         while let Ok(event) = handle.event_rx.recv().await {
             // Check timeout
             if let Some(timeout) = timeout_duration

cortex-engine/src/tasks/snapshot.rs

@@ -292,7 +292,7 @@ impl SnapshotManager {
             match state {
                 FileState::Exists {
                     content,
-                    permissions: _,
+                    permissions,
                     ..
                 } => {
                     // Create parent directories
@@ -303,7 +303,6 @@ impl SnapshotManager {
                     // Write content
                     fs::write(path, content)?;
 
-                    // Set permissions
                     #[cfg(unix)]
                     if let Some(mode) = permissions {
                         use std::os::unix::fs::PermissionsExt;