fix(web): keep a staged file hidden until a preview generated after the stage lands

[MTVaught]

Problem

Staging files in quick succession in the Unstaged view let an already-staged file flash back. The optimistic hide from #101 was tied to the preview on screen: staging A started a refresh, staging B during that refresh joined the same hidden set, and when A's refresh landed the set was discarded, so B showed until its own refresh arrived.

Fix

Both sides now stamp the server clock, so no client clock is involved:

• vcs.stagePaths returns the time the index update completed.
• The diff preview stamps generatedAt before reading the repository instead of after.
• A hidden file stays hidden until a preview generated after its stage completed lands. A refresh that started before the stage finished can no longer resurrect it. Entries are scoped to the thread and filter, and a failed command still unhides the file with the error toast.

Follow-up to #100 and #101.

Built with Claude Fable 5.1 via Claude Code in T3 Code.

[github-actions]

Thread transfer impact

✅ Thread transfer remains within every enforced ceiling.

Provider	Metric	Main baseline	This PR	Impact	PR ceiling
Codex	Total thread wire	13.6 KiB	13.5 KiB	−114 B (−0.8%)	15.1 KiB	✅
Codex	Thread snapshot wire	7.1 KiB	7.1 KiB	+2 B (+0.0%)	7.3 KiB	✅
Codex	Live turn WebSocket wire	6.5 KiB	6.4 KiB	−116 B (−1.7%)	7.8 KiB	✅
Codex	Live turn WebSocket decoded	57.0 KiB	56.2 KiB	−866 B (−1.5%)	66.4 KiB	✅
Codex	Live turn messages	9	8	−1 (−11.1%)	21	✅
Claude	Total thread wire	13.6 KiB	13.5 KiB	−122 B (−0.9%)	15.1 KiB	✅
Claude	Thread snapshot wire	7.1 KiB	7.1 KiB	+5 B (+0.1%)	7.3 KiB	✅
Claude	Live turn WebSocket wire	6.6 KiB	6.4 KiB	−127 B (−1.9%)	7.8 KiB	✅
Claude	Live turn WebSocket decoded	57.9 KiB	57.0 KiB	−928 B (−1.6%)	66.4 KiB	✅
Claude	Live turn messages	10	8	−2 (−20.0%)	21	✅

Baseline: 3332115 · PR result: 1b543c3 · Source CI: success

Scenario and decoded snapshot size

10 historical turns, 5 command tools per turn, 878.9 KiB retained MCP result per historical turn, and a 1.05 MiB retained result in the measured turn.

• Codex decoded thread snapshot: 113.9 KiB
• Claude decoded thread snapshot: 114.6 KiB

Updated in place by a trusted workflow. PR artifacts are strictly validated and never executed.