fix: make _merge_toml_fragment and _remove_toml_entries use atomic writes

[Quratulain-bilal]

Problem

Both _merge_toml_fragment and _remove_toml_entries used write_text() which truncates the file before writing. A crash or power loss mid-write leaves a partial TOML file.

Fix

Now uses empfile.mkstemp + os.replace for atomic writes, matching the pattern used elsewhere in the codebase.

[Copilot]

Pull request overview

Updates TOML event configuration writes to use temporary files and atomic replacement.

Changes:

• Adds tempfile support.
• Converts TOML merge/removal rewrites to mkstemp and os.replace.
• Cleans up staged files on failure.

Show a summary per file

File	Description
src/specify_cli/events.py	Adds atomic TOML rewrite paths.

Review details

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Suppressed comments (2)

src/specify_cli/events.py:1775

• This teardown path also replaces an existing TOML file with mkstemp's 0600 mode. Removing Spec Kit entries from a group-readable or group-writable config therefore changes access for unrelated user content. Preserve the destination's existing mode before os.replace, as the workflow registry writer does in src/specify_cli/workflows/catalog.py:162-188.

    fd, tmp = tempfile.mkstemp(
        dir=str(dst.parent), prefix=f".{dst.name}.", suffix=".tmp"
    )

src/specify_cli/events.py:1779

• The removal rewrite has the same durability gap: os.replace is namespace-atomic, but the staged bytes and rename are not made durable before returning. Because this PR explicitly claims protection from power loss, sync the staged file before replacement and the parent directory afterward via the same platform-aware helper.

        with os.fdopen(fd, "w", encoding="utf-8") as f:
            f.write(cleaned)
        os.replace(tmp, dst)

• Files reviewed: 1/1 changed files
• Comments generated: 3
• Review effort level: Balanced