[BUG] Desktop: deleting a session from the sidebar now permanently deletes its local transcript (since Claude Code 2.1.284), wiping usage stats for that day

What changed

Since the Desktop update on 2026-09-29 (Claude Desktop 2.16120.0, bundled Claude Code 2.1.284, previously 2.1.281), deleting a session from the Code tab sidebar also removes, with no undo:

• the transcript .jsonl under ~/.claude/projects/
• that session's prompts in ~/.claude/history.jsonl
• its file-history/ and session-env/ entries

Before this update, deleting a session only hid it: the app wrote a deleted_<id> marker under claude-code-sessions/, and the transcript stayed on disk.

Evidence (macOS, Darwin 27.0.0)

• Sessions I deleted on 2026-09-28 (on 2.1.281): their transcripts are still on disk.
• Sessions I deleted on 2026-09-29 21:58 and 2026-09-30 12:14 / 13:58 / 18:11 / 19:12 (on 2.1.284): no transcript, no history.jsonl entries, no file-history. The sessions definitely existed: they made dozens of git commits in my repos during those hours.
• cleanupPeriodDays is set to 9999999999, so this is not the retention sweep.
• A Time Machine backup taken at 21:07 the same evening already lacks them, so the files are removed at the moment of deletion.

I inferred this from the evidence above and have not reproduced it with a throwaway session.

Impact

• The Desktop usage heatmap shows 2026-09-30 as empty, although I worked all day. The stats cache only computes completed days, so a session deleted the same day is never counted, and there is no way to rebuild it.
• I set cleanupPeriodDays high specifically to keep my history. Deleting a session from the sidebar now silently overrides that.
• I delete sessions to keep the sidebar short, not to erase my history. Those are two different things, and until 2.1.284 the app treated them as different.

What I'm asking for

1. Deleting a session from the sidebar should only remove it from the sidebar, as it did before 2.1.284. The local transcript, prompt history and usage stats should stay.
2. If some users want deletion to erase the transcript too, make that an opt-in setting (for example "Also delete local transcripts when deleting a session"), off by default. A warning dialog does not solve this: I want to be able to clear the sidebar without ever losing the transcript.
3. Mention behavior changes like this in the release notes.

Related: #62476 (transcripts deleted silently), #94479 (stats history loss when transcripts are gone).