fix: honour store_failed for negative exit codes and daemon mode

[jerry7991]

Summary

store_failed = false was still keeping two classes of failed commands in history:

1. Signal kills (negative exit codes) — crates/atuin/src/command/client/history.rs:511 used exit > 0, so anything that came in as a negative exit (e.g. Ctrl+C-interrupted runs, which atuin already supports recording per fix: record negative exit codes #821) slipped past the filter.
2. Daemon mode — the daemon's EndHistory RPC handler never consulted store_failed, so users running daemon.enabled = true had every non-zero exit persisted regardless of their setting.

Changes

• handle_end: change the predicate to exit != 0 so negative exit codes are also dropped.
• atuin-daemon history component: check handle.settings().await.store_failed inside end_history; when it's false and the exit is non-zero, remove the entry from the running map and return early without writing to the local DB or pushing to the record store.
• Add four unit tests covering (store_failed, exit) combinations: failed+disabled, signal-killed+disabled, success+disabled, failed+enabled.
• Touch up the store_failed config doc to mention signal kills and daemon mode.

Why

Reported by a user who had store_failed = false but still saw failed commands appearing in atuin search. The behaviour was due to the two gaps above. The local-path bug was introduced in #2284 when the original != was tightened to > on the (incorrect) assumption that exit codes are always 0–255; the daemon-path gap was there from the original daemon implementation.

Test plan

• cargo test -p atuin --bin atuin handle_end — 4 new tests pass
• cargo test -p atuin --bin atuin — full atuin suite green (218 passed)
• cargo test -p atuin-daemon — daemon lifecycle suite green (5 passed)
• cargo clippy -p atuin -p atuin-daemon --no-deps — clean
• cargo fmt --check -p atuin -p atuin-daemon — clean

[github-actions]

Fossier: Manual Review Requested

@jerry7991 is a new contributor. A maintainer should review this PR before merging.

Score Breakdown

Total Score: 67.1/100 | Confidence: 100% | Outcome: REVIEW

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public_repos	32	1.00	0.05
contribution_history	32	0.16	0.05
follower_ratio	0.7	0.35	0.05
bot_signals	False	0.50	0.04
open_prs_elsewhere	2	0.75	0.09
closed_prs_elsewhere	0	1.00	0.10
merged_prs_elsewhere	13	1.00	0.08
prior_interaction	0	0.00	0.08
activity_velocity	1	1.00	0.08
pr_content	...	1.00	0.08
commit_email	no_email	0.50	0.04
pr_description	...	0.55	0.05
repo_stars	29796	0.30	0.04
org_membership	0	0.20	0.03
commit_verification	...	0.30	0.04
contributor_stars	26	0.52	0.04

[greptile-apps]

Greptile Summary

This PR makes store_failed = false apply consistently to non-zero command exits. The main changes are:

• Treat negative exit codes as failed in the local history end path.
• Drop failed daemon-mode history entries before DB and record-store writes.
• Add unit coverage for failed, signal-killed, successful, and allowed-failure cases.
• Update the config docs to mention signal kills and daemon mode.

Confidence Score: 5/5

This looks safe to merge.

• No blocking issues found in the changed code.
• The daemon path removes the in-memory running entry before returning.
• The local path reuses the existing soft-delete behavior for failed commands.

Important Files Changed

Filename	Overview
crates/atuin/src/command/client/history.rs	Updates the local failed-command filter and adds focused tests for store_failed behavior.
crates/atuin-daemon/src/components/history.rs	Adds daemon-side filtering so non-zero exits are not persisted when failed-command storage is disabled.
docs/docs/configuration/config.md	Clarifies that store_failed = false applies to all non-zero exits and daemon mode.

_{Reviews (1): Last reviewed commit: "fix: honour store_failed for negative ex..." | Re-trigger Greptile}