fix(coding-agent): report the shell exit code when bash times out after the shell exited (#11813)

Fixes #11613.

## Problem

The bash tool waits for stdout/stderr to close, not only for the shell
to exit (#5303). A background process that inherited those pipes and
keeps writing keeps the tool waiting after the shell exited. When the
timeout then hits, the tool reported only `Command timed out after N
seconds`.

Example, timeout 3s:

```bash
bash -c 'while true; do echo tick; sleep 0.05; done' & sleep 1; echo boom >&2; exit 1
```

The shell exits with code 1 after ~1s. The tool still times out at the
deadline, because the loop is still writing to its output. Both facts
are true: the command failed with code 1, and something it started was
still running at the timeout. The old message dropped the first, so the
model read a failed command as a slow one and retried with a longer
timeout, which never helps here.

## Fix

The timeout stays a timeout, since the tool did hit its deadline while
background processes were still writing. When the shell had already
exited before the deadline, the message now also says so:

```
Command timed out after 3 seconds. The shell exited with code 1 after 1.1 seconds, but background processes it started kept writing output until the timeout.
```

A shell still running at the deadline keeps the plain `Command timed out
after N seconds`.

The local backend throws a module-private `ShellTimeoutError` with the
message `timeout:<seconds>` as before, so custom `BashOperations` that
throw `timeout:N` are unaffected.

## Behavior per platform

- Linux and macOS: the shell runs in its own process group (`detached:
true`). At the deadline `kill(-pgid)` still reaches the background
processes after the shell exited, the pipes close, and the tool returns
at the deadline. Tested on Linux; macOS uses the same mechanism and
matches the macOS repros in the issue.
- Windows: still not fully solved. At the deadline `taskkill /T /PID
<shell>` fails with `process not found`, because the shell pid is gone.
Walking parent pids does not help: Git's `bin\bash.exe` is a launcher
for `usr\bin\bash.exe`, and the orphaned loop's parent is that
already-exited inner bash, not the pid pi holds. The tool keeps reading
until the output pauses for 100ms. Measured with Git Bash: the message
is now correct, but the tool returned after 14s instead of 3s; with a
loop that never pauses it never returns. This PR only fixes the
reporting.

## Same pattern elsewhere

- `packages/durable/src/env/node.ts` (`NodeExecutionEnv.exec`): same
code, same false `timeout:N` after the shell exited. Same Windows
limitation.
- `packages/coding-agent/src/core/exec.ts` (`pi.exec` for extensions):
the timeout sends SIGTERM/SIGKILL to the direct child only, no process
group. A descendant that keeps writing keeps the call waiting past the
timeout on every platform, and the result has `killed: true` even when
the child had already exited with its own code.
- `packages/coding-agent/src/core/package-manager.ts` (capture commands
for git/npm): waits for `close` and kills only the direct child on
timeout, so a descendant holding the pipes makes the timeout ineffective
on every platform, even when the descendant writes nothing.
- `packages/mcp/src/transports/stdio.ts`: on Windows, closing a server
that already exited skips taskkill, so children holding its pipes
survive. The code documents this as a known limitation.

Possible follow-up for Windows and the cases above: once the deadline
passed, stop waiting for the pipes (destroy our ends). On Windows this
also ends most writers, which die from a broken pipe (tested with Git
Bash).

## Tests

- `test/suite/regressions/11613-bash-timeout-after-shell-exit.test.ts`
(Unix only; it would hang on Windows for the reason above): background
writer after the shell exits with code 3, and a shell still running at
the deadline. The first case fails without the fix.
- Checked manually on Windows 11 with Git Bash through the built bundle:
both messages are as above.
- `npm run check`, `test/tools.test.ts`, the #5303 and #5208
regressions, `bash-close-hang-windows`, `powershell-tool`,
`shell-kill-process-tree`.

This PR description is AI-generated.

packages/coding-agent/CHANGELOG.md

@@ -19,6 +19,7 @@
 
 ### Fixed
 
+- Fixed the bash tool reporting only `Command timed out` when the command had already exited but a background process it started kept writing to its output until the timeout. The error now also reports the shell's exit code and when it exited ([#11613](https://github.com/earendil-works/pi/issues/11613))
 - Images in steering and follow-up messages, including `prompt()` while streaming, are now resized like images in idle prompts instead of being sent and saved at full size ([#11738](https://github.com/earendil-works/pi/issues/11738))
 - A failed token refresh of an MCP connection no longer registers an OAuth client or replaces the PKCE verifier of a sign-in in progress, which made that sign-in fail. MCP sign-in now refreshes the stored tokens with the stored client even when the loopback callback port changed, instead of registering a new client and opening the browser. Ctrl+C in `/mcp` and the `--timeout` of `pi mcp login` now also stop a sign-in while it waits up to 25 seconds for another pi process's token refresh, and a refresh lock that fails for another reason than that wait now fails the sign-in instead of opening the browser.
 - Fixed `pi mcp list` reporting MCP servers with `"auth": { "provider": "<provider>" }`, such as Radius, as needing sign-in although the provider was signed in: the shell command sent no token. It now sends the provider's `/login` token and refreshes it when it expired. For these servers the sign-in hint names `/login <provider>` instead of `pi mcp login`, and `pi mcp login` and `pi mcp logout` point to `/login` and `/logout` instead of failing with "does not use OAuth"