mcp: refresh last_activity during long bundle processing (#278)

[justrach]

Diagnosis

`idleWatchdog` in `main.zig` closes stdin when `now - last_activity > idle_timeout_ms` (10 min). But `last_activity` is only updated once per incoming message — right after `readLineBuf` at `mcp.zig:474`. Inside a single `codedb_bundle` call that takes longer than 10 minutes (many slow sub-ops, or ops that shell out to `codedb_remote` / `codedb_tree` on huge repos), the clock stays frozen at message-arrival time. At the 10-minute mark the watchdog closes stdin mid-processing.

The main thread finishes the bundle and writes the response fine (stdout is untouched), but the client — whose write-end of the stdin pipe just got `EPIPE`d — reports "Transport closed" on its next tool call. That matches the reporter's note in #278 that the issue shows up on "long enough sessions".

Fix

Stamp `last_activity` at bundle start AND at the end of each completed sub-op inside `handleBundle`. Every sub-op is bounded by its own logic, so the watchdog can only fire when the main thread truly has nothing in flight.

No change to the idle path: a bundle that completes in under 10 min doesn't touch `last_activity` beyond what was already there; sessions that actually go idle still get reaped on the same schedule.

Scope

• 9 lines added to `src/mcp.zig` inside `handleBundle`.
• No test change — this is a timing/watchdog interaction and the existing idle-watchdog tests cover the reaping path; covering this would need a multi-minute slow sub-op mock.
• Non-bundle code paths unchanged. If "Transport closed" still surfaces on single-tool calls we'll need a separate repro — this is the most obvious trigger given the reporter's description.

Test plan

• `zig build` green
• Existing `codedb_bundle` behavior unchanged on short bundles (tested locally)
• Anecdotal: the original reporter should see "Transport closed" go away on long bundle sessions. Would help to get confirmation before we call Occasional "Transport closed" MCP crash #278 fully closed.

🤖 Generated with Claude Code

[github-actions]

Benchmark Regression Report

Threshold: 10.00%

Tool	Base (ns)	Head (ns)	Delta	Status
codedb_bundle	495355	527594	+6.51%	OK
codedb_changes	57127	59423	+4.02%	OK
codedb_deps	9461	9258	-2.15%	OK
codedb_edit	6009	6495	+8.09%	OK
codedb_find	65189	67279	+3.21%	OK
codedb_hot	99208	101167	+1.97%	OK
codedb_outline	243505	240650	-1.17%	OK
codedb_read	86757	92590	+6.72%	OK
codedb_search	180897	179664	-0.68%	OK
codedb_snapshot	2710820	2601748	-4.02%	OK
codedb_status	219093	215314	-1.72%	OK
codedb_symbol	60097	61571	+2.45%	OK
codedb_tree	81844	83382	+1.88%	OK
codedb_word	70821	72105	+1.81%	OK