refactor: simplify session lifecycle and zellij runtime

[AgentWrapper]

Summary

This PR simplifies the agent session lifecycle model and removes a large amount of now-unneeded runtime, notification, and storage plumbing.

Lifecycle/session model

• Removes the canonical lifecycle/decide state machine and associated domain types/tests.
• Removes notification domain/storage/rendering/dedupe code that depended on that lifecycle model.
• Stores only durable session facts needed for status derivation: activity_state, activity_source, activity_last_at, and boolean is_terminated.
• Derives user-facing session status at read time from session facts plus PR facts.
• Keeps PR-driven agent nudges in lifecycle for CI failures, merge conflicts, and review feedback.

Runtime simplification

• Removes tmux runtime adapter, tests, and related configurability.
• Standardizes runtime behavior on Zellij only.
• Removes per-session runtime_name/runtime configurability from storage and wiring.
• Narrows session/runtime interfaces so session creation depends only on create/destroy, while liveness remains with reaper/terminal paths.
• Adds Zellij version validation to ao doctor using the runtime's minimum supported version.

Storage/sqlite cleanup

• Removes notification tables/queries/store code.
• Moves SQLite store implementation files into backend/internal/storage/sqlite/store.
• Regenerates sqlc with stronger Go types for IDs, enums, booleans, and PR/session fields.
• Adds npm run sqlc as the explicit sqlc generation workflow.
• Keeps generated storage rows internal to sqlite and uses domain types for app-level PR/session models.

Ports/domain/API cleanup

• Moves PR persistence models into domain and keeps ports focused on boundary contracts/DTOs.
• Removes unused broad port interfaces and narrows package-local interfaces where possible.
• Splits mixed observation DTOs into PR-specific and runtime/activity-specific files.
• Cleans stale docs/comments around lifecycle, daemon, terminal, and status behavior.
• Renames HTTP terminal mux implementation files/symbols for clarity while preserving the /mux route.
• Makes HTTP/terminal logger dependencies tolerate nil by falling back to slog.Default().

CLI and docs

• Updates docs to reflect Zellij-only runtime support and derived session status.
• Makes CLI commands reject unexpected positional arguments consistently.
• Keeps ao doctor from opening/migrating SQLite; daemon remains the only DB migrator/writer.

Testing

• npm run sqlc
• npm run lint
• cd backend && go test -race ./...

[greptile-apps]

Greptile Summary

This PR is a substantial simplification of the session lifecycle model: the canonical CanonicalSessionLifecycle state machine (with its multi-field session state, termination reason, detecting quarantine, and is_alive flag) is replaced by two persisted facts — activity_state and is_terminated. User-facing status is derived at read time from those facts plus PR data in the pr table. The notifications subsystem (domain, storage, schema, sqlc, wiring) and the tmux runtime adapter are removed entirely, standardising on Zellij only.

• The lifecycle.Manager is slimmed to two write-paths (MarkSpawned, MarkTerminated) plus observation appliers; the pr.Manager is a new package that persists PR observations and forwards merge/nudge events to the LCM; the reaper loses its RuntimeRegistry and uses a single injected ports.Runtime.
• Migration 0004_simplify_session_state.sql drops session_state, termination_reason, is_alive, detecting columns, and runtime_name, adds is_terminated, and rewrites the session CDC triggers; the notifications migration 0002 is deleted and the notifications table is dropped in the 0004 Up path.

Confidence Score: 5/5

Safe to merge; the simplification is well-executed and the migration correctly handles both fresh and existing databases with IF EXISTS guards throughout.

The lifecycle model refactor correctly replaces the multi-field state machine with two persisted facts (activity_state + is_terminated) and derives display status at read time. The migration Up/Down paths are symmetric and cover both upgrade and fresh-DB cases. The anti-flap mechanism (ProbeDead+ProbeDead required, recent-activity window) is simpler than the old detecting quarantine but still protects against transient false positives. No logic errors or data-corruption paths were found in the changed code.

reactions.go — the sendOnce dedup state is not session-scoped and never pruned; low practical risk given PR URL uniqueness, but worth addressing before this path sees heavy use.

Important Files Changed

Filename	Overview
backend/internal/lifecycle/reactions.go	Reduced to agent-only nudges via sendOnce; dedup state (seen/attempts maps) is not session-scoped and is never pruned on session termination or restart
backend/internal/lifecycle/manager.go	Simplified to MarkSpawned/MarkTerminated plus ApplyActivitySignal/ApplyRuntimeObservation; mutate pipeline correctly diffs before writing
backend/internal/storage/sqlite/migrations/0004_simplify_session_state.sql	Correctly drops old session columns/notifications and adds is_terminated; IF EXISTS guards cover both fresh-DB and upgrade paths; Down section restores pre-migration schema with best-effort state mapping
backend/internal/pr/manager.go	New package cleanly separates PR persistence from lifecycle; correctly sequences write to terminate/nudge; nil guards on sessions and lifecycle fields are test-only affordances
backend/internal/domain/status.go	DeriveStatus simplified to is_terminated+PR branch then activity-state fallthrough; removes StatusSpawning/StatusDetecting/StatusErrored/StatusKilled/StatusDone/StatusCleanup
backend/internal/observe/reaper/reaper.go	Reaper simplified: RuntimeRegistry removed, single ports.Runtime injected; probeOne builds facts correctly; no longer calls TickEscalations
backend/internal/storage/sqlite/store/session_store.go	New session store layer with clean domain-to-gen mapping; normalActivity helper ensures default state/source/timestamp are always set before writes
backend/internal/storage/sqlite/store/pr_facts.go	ListPRFactsForSession issues one ListPRComments query per PR, an N+1 pattern that is benign for typical single-PR sessions but could scale poorly
backend/internal/lifecycle/decide_bridge.go	runtimeClearlyDead replaces the full probe decider; correctly requires both Runtime and Process == ProbeDead plus no recent activity before marking dead
backend/internal/session/manager.go	Kill/Restore/Cleanup updated to use IsTerminated boolean; displayPR helper correctly prefers an open PR over merged/closed ones when deriving display status

Sequence Diagram

sequenceDiagram
    participant GH as GitHub Tracker
    participant PRM as pr.Manager
    participant LCM as lifecycle.Manager
    participant Store as SQLite Store
    participant Reaper as Reaper

    Note over GH,Reaper: PR observation flow (new model)
    GH->>PRM: ApplyObservation(id, obs)
    PRM->>Store: WritePR(row, checks, comments)
    alt "obs.Merged == true"
        PRM->>LCM: MarkTerminated(id)
        LCM->>Store: "UpdateSession is_terminated=true activity=exited"
    else obs open or CI failing or review
        PRM->>LCM: ApplyPRObservation(id, obs)
        LCM->>Store: GetSession(id)
        LCM-->>LCM: sendOnce(key, sig, msg)
        LCM->>LCM: messenger.Send(id, msg)
    end

    Note over Reaper,LCM: Runtime liveness probe (new model)
    Reaper->>Store: ListAllSessions()
    loop each non-terminated session
        Reaper->>Reaper: zellij.IsAlive(handle)
        alt ProbeDead and no recent activity
            Reaper->>LCM: ApplyRuntimeObservation(id, facts)
            LCM->>Store: "UpdateSession is_terminated=true activity=exited"
        end
    end

    Note over LCM,Store: Status derivation on read
    Store-->>LCM: SessionRecord plus PRFacts list
    LCM-->>LCM: displayPR selects best PRFacts
    LCM-->>LCM: DeriveStatus returns SessionStatus

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