fix: auto-assign after merge, persistent server logs, remove duplicate pnpm install

- Call auto_assign_available_work at end of merge_agent_work so the next
  story gets picked up without waiting for the PTY exit handler
- Add persistent file logging to .story_kit/logs/server.log so server
  logs survive restarts
- Remove duplicate pnpm install block in run_squash_merge

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

server/src/log_buffer.rs

@@ -7,6 +7,9 @@
 //! `get_server_logs` MCP tool.
 
 use std::collections::VecDeque;
+use std::fs::OpenOptions;
+use std::io::Write;
+use std::path::PathBuf;
 use std::sync::{Mutex, OnceLock};
 
 const CAPACITY: usize = 1000;
@@ -68,12 +71,22 @@ impl LogEntry {
 
 pub struct LogBuffer {
     entries: Mutex<VecDeque<LogEntry>>,
+    log_file: Mutex<Option<PathBuf>>,
 }
 
 impl LogBuffer {
     fn new() -> Self {
         Self {
             entries: Mutex::new(VecDeque::with_capacity(CAPACITY)),
+            log_file: Mutex::new(None),
+        }
+    }
+
+    /// Set the persistent log file path. Call once at startup after the
+    /// project root is known.
+    pub fn set_log_file(&self, path: PathBuf) {
+        if let Ok(mut f) = self.log_file.lock() {
+            *f = Some(path);
         }
     }
 
@@ -86,6 +99,15 @@ impl LogBuffer {
             message,
         };
         eprintln!("{}", entry.colored_formatted());
+
+        // Append to persistent log file (best-effort).
+        if let Ok(guard) = self.log_file.lock()
+            && let Some(ref path) = *guard
+            && let Ok(mut file) = OpenOptions::new().create(true).append(true).open(path)
+        {
+            let _ = writeln!(file, "{}", entry.formatted());
+        }
+
         if let Ok(mut buf) = self.entries.lock() {
             if buf.len() >= CAPACITY {
                 buf.pop_front();
@@ -188,6 +210,7 @@ mod tests {
     fn evicts_oldest_at_capacity() {
         let buf = LogBuffer {
             entries: Mutex::new(VecDeque::with_capacity(CAPACITY)),
+            log_file: Mutex::new(None),
         };
         // Fill past capacity
         for i in 0..=CAPACITY {