metrics_compare_base: catch TimeoutExpired; fix code-size skill docs

- run() now catches subprocess.TimeoutExpired (only triggered by `cmake --build`'s
  timeout=600) and returns CompletedProcess(rc=124) so the caller falls through to
  error reporting and worktree cleanup instead of crashing with a traceback.
- code-size SKILL.md: document the actual default filter (per-side absolute
  <checkout>/src/ path, not the old `tinyusb/src` substring) and adjust the
  reporting guidance to match what the report rows actually contain.

Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>

2 files changed, 12 insertions, 4 deletions

diff --git a/.claude/skills/code-size/SKILL.md b/.claude/skills/code-size/SKILL.md
index e12a30d86..f3c51ccfa 100644
--- a/.claude/skills/code-size/SKILL.md
+++ b/.claude/skills/code-size/SKILL.md
@@ -30,7 +30,7 @@ Infer from the user's request:
 - **Example:** named example → `-e <group>/<name>` (e.g. `-e device/cdc_msc`). "All examples" → omit `-e`.
 - **Bloaty:** only with `-e`. Use when the user wants a section/symbol-level breakdown for a single binary.
 - **Base ref:** default `master`. Override with `--base-branch <ref>` (tag or commit also works).
-- **Filter:** default `tinyusb/src` (only counts TinyUSB stack code, not example/BSP). Change only if asked.
+- **Filter:** default is the absolute path of each side's `<checkout>/src/` directory, which uniquely identifies TinyUSB stack code without matching vendored deps that also have a `src/` (e.g. `pico-sdk/src/`). Override with one or more `-f SUBSTRING` flags to use repo-relative substrings instead. Change only if asked.
 
 ## Common invocations
 
@@ -72,5 +72,5 @@ Use timeouts ≥ 10 minutes (600000 ms) for `--ci`.
 
 After running:
 - Show the markdown report's summary table to the user.
-- Highlight any rows with non-zero diff in `tinyusb/src` paths — those are the actual stack-size deltas.
+- Highlight any rows with non-zero `% diff` — under the default filter every row is a TinyUSB stack source file (e.g. `usbd.c`, `cdc_device.c`, `dcd_<port>.c`), so any non-zero delta is a real stack-size impact.
 - If the diff is unexpected, follow up with a single-example `--bloaty` run to localize.
diff --git a/tools/metrics_compare_base.py b/tools/metrics_compare_base.py
index 0fb767bb7..a541dae79 100644
--- a/tools/metrics_compare_base.py
+++ b/tools/metrics_compare_base.py
@@ -37,12 +37,20 @@ verbose = False
 
 
 def run(cmd, **kwargs):
-    """Run a command. cmd must be a list (no shell=True)."""
+    """Run a command. cmd must be a list (no shell=True). On `timeout=`-induced
+    TimeoutExpired, return a CompletedProcess with rc=124 instead of letting the
+    exception propagate, so the caller can fall through to error reporting and
+    worktree cleanup rather than crashing with a traceback."""
     if not isinstance(cmd, list):
         raise TypeError('run() requires a list, got str — fix the caller')
     if verbose:
         print(f'  $ {" ".join(shlex.quote(str(c)) for c in cmd)}')
-    return subprocess.run(cmd, capture_output=True, text=True, **kwargs)
+    try:
+        return subprocess.run(cmd, capture_output=True, text=True, **kwargs)
+    except subprocess.TimeoutExpired as e:
+        msg = f'Command timed out after {e.timeout}s: {" ".join(shlex.quote(str(c)) for c in cmd)}'
+        stderr = (e.stderr or '') + ('\n' if e.stderr else '') + msg
+        return subprocess.CompletedProcess(cmd, 124, stdout=(e.stdout or ''), stderr=stderr)
 
 
 def symlink_deps(main_root, worktree_dir):