Bash mutations can leave FileTime stale and break same-session edit/write #14183

Problem

When a session reads a file, then modifies that same file using the bash tool, later edit/write calls in the same session can fail with:

File <path> has been modified since it was last read.

This causes retry loops because the file was changed by the same session, but FileTime remains stale.

Reproduction

1. Read a file via Read tool.
2. Modify the file via bash (for example: printf 'new' > file.txt).
3. Run Edit or Write on that file in the same session.
4. Observe FileTime.assert() stale-read failure.

Expected behavior

If a file already tracked in the session is changed by bash, the session FileTime should be refreshed so subsequent same-session edits/writes do not fail immediately.

Actual behavior

bash does not update FileTime, so assert() can reject valid same-session follow-up edits/writes.

Notes

This is different from bypassing safety checks globally. The expectation is to preserve read-before-write protection while avoiding false-positive stale-read failures for same-session shell mutations.