fix: rebase onto upstream/dev — Effect-ification integration (Phase 4)

[e6qu]

Summary

Integrates all remaining upstream changes by replaying 41 upstream commits on top of origin/dev, closing the upstream gap entirely:

• 44 commits ahead of dev (41 upstream + 3 integration fixes)
• Integrates all upstream Effect-ification refactors (LayerMap, SkillService, FileService, VcsService, FormatService, FileTimeService, FileWatcherService, SnapshotService), model updates, and community fixes
• Git auto-dropped 9 commits already present via our backports (B1-B22)

Conflict resolutions

• skill.ts: Kept upstream's SkillService Effect pattern, re-added our Meta/Loaded types and meta() method on top
• pty-session.test.ts: Kept our improved waitForBus (event-driven) over upstream's polling wait
• llm.ts: Resolved trivial field-ordering conflict, removed duplicate permission field
• copilot.ts, provider.ts: Accepted ours (already backported)
• config.ts, prompt.ts, line-comment*: Used already-resolved versions from initial rebase pass
• account.ts: Removed duplicate isActiveOrgChoice (upstream already had it)

Verification

• bun typecheck — 0 errors across all 13 packages
• bun test — 1430 pass, 0 fail, 8 skip

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Upstream contributors integrated

Contributor	Contributions
Kit Langton	refactor(instance): LayerMap (#17544), effectify FileWatcherService (#17827), VcsService (#17829), FileTimeService (#17835), FormatService (#17675), FileService (#17845), SkillService (#17849), SnapshotService (#17878), prompt schema debug logs (#17812)
Frank	zen: model updates, error logging, deprecate gemini 3 pro
Luke Parker	fix(app): prompt tooltip (#17857), test deflakes (#17881, #17859), fix(ci): Windows linker (#17751), fix(opencode): test ID (#17745)
Ariane Emory	fix: apply_patch EDIT_TOOLS filter (#18009)
Shoubhit Dash	fix: inline review comment layout (#17948), question option wrapping (#17782)
David Hill	tweak(ui): sidebar empty state (#17971), remove open label (#17512)
Aiden Cline	fix: copilot enterprise (#17847), vcs watcher (#17673), chore: denounce ai spammer (#17901)
Kyle Altendorf	docs: snapshot config annotation (#17861), fix(tui): dialog escape selection (#16779)
AbigailJixiangyuyu	fix(windows): /editor support (#17146)
Brendan Allan	app: inherit owner on prompt session (0afeaea)
DS (Tarquinen)	fix: message transforms during compaction (#17823)
Johannes Loher	fix: context_length_exceeded error handling (#17748)
Michal Šlesár	fix(app): agent switch thinking level (#17470)
Jason Quense	fix: preserve prompt tool enables (#17064)
OpeOginni	docs: mark tools config deprecated (#17951)
Erik Engervall	docs: firecrawl ecosystem (#17672)
Orlando Ascanio	docs(es): Spanish translation fixes (#17563)

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Integration fix commits (by @e6qu)

Commit	Description
749fd71	fix: post-rebase cleanup — remove duplicate, update status
2fbf8c6	chore: linter formatting + SDK gen from upstream rebase
34977e5	fix: remove duplicate permission field in StreamInput

Test plan

• bun typecheck — 0 errors
• bun test — 1430 pass, 0 fail
• Smoke-test TUI: context editing, side threads, /cost command