fix: harden the bundle lifecycle per code review

The path-escape guard that uninstall applies to recorded paths now also
covers update's obsolete-file deletion through a shared check, so a
tampered store cannot turn either delete site into an arbitrary file
removal. Updates gain a working non-interactive path: --yes now applies
to --update-bundle (locally modified files, obsolete files, and modified
mcp entries are all kept; everything else refreshes), owned mcp entries
whose recorded hash still matches the local entry take the remote side
without prompting, and the non-TTY conflict bails name the flag that
actually works per surface. An update records its new commit and version
only after files and mcp entries land, so an aborted update cannot claim
content it never wrote. The store gains a version field and rejects
stores from newer builds, the corrupt-store error no longer advises the
removal that would forfeit ownership tracking, and duplicate records
tracking one source abort a rename instead of overwriting a record.
Reinstalling from a source URL reclassifies owned unmodified files as
silent refreshes just like updates. git runs with GIT_TERMINAL_PROMPT=0
and a null stdin so private or mistyped URLs fail instead of hanging.
File comparison fills buffers fully before comparing, deleting an
obsolete file prunes emptied directories, mcp.json backfill uses the
fsynced atomic writer, --list-bundles no longer triggers builtin
backfill, bundle-name completion logs store errors instead of swallowing
them and offers --yes, and REPL .uninstall rejects unknown flags.

src/function/mod.rs

@@ -493,9 +493,8 @@ impl Functions {
 
         let serialized =
             serde_json::to_string_pretty(&merged).context("failed to serialize merged mcp.json")?;
-        let tmp = file_path.with_extension("json.tmp");
-        fs::write(&tmp, &serialized).context("failed to write temporary mcp.json")?;
-        fs::rename(&tmp, &file_path).context("failed to finalize mcp.json")?;
+        write_file_atomic(&file_path, &serialized, None)
+            .context("failed to write merged mcp.json")?;
 
         if !added.is_empty() {
             println!("  + new MCP servers: {}", added.join(", "));