chore: unify and centralize agent configuration in .agent/

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+# SESSION_STATE.md
+
+## Current Task Goal
+ADR-007 implementation: Epic→Story→Task→Subtask hierarchy, project registry, Doot integration
+
+## Status: IN_PROGRESS
+
+---
+
+## Completed Items
+
+| Step | Description | Test / Verification |
+|------|-------------|---------------------|
+| Phase 1 | Doot dead code removal: Bug struct, BugToAtom, bug store methods, bug handlers, bug routes, bugs.html template, TypeNote, AddMealToPlanner stub | `go test ./...` in /workspace/doot — all pass (2 pre-existing failures unrelated) |
+| Phase 2 | Claudomator project registry: `task.Project` type, storage CRUD + UpsertProject, seed.go, API endpoints (GET/POST /api/projects, GET/PUT /api/projects/{id}), legacy AgentConfig.ProjectDir/RepositoryURL/SkipPlanning fields removed, container.go fallback removed, fallbackGitInit removed, processResult changestats extraction removed (pool-side only) | `TestCreateProject`, `TestListProjects`, `TestUpdateProject`, `TestProjects_CRUD` — all pass |
+
+---
+
+## Next Steps (Claudomator tasks created)
+
+Phases 3–6 are queued as Claudomator tasks. See `ct task list` or the web UI.
+
+| Task ID | Phase | Status | Depends On |
+|---------|-------|--------|------------|
+| f8829d6f-b8b6-4ff2-9c1a-e55dd3ab300e | Phase 3: Stories data model | PENDING | — |
+| c8a0dc6c-0605-4acb-a789-1155ad8824cb | Phase 4: Story execution and deploy | PENDING | Phase 3 |
+| faf5a371-8f1c-46a3-bb74-b0df1f062dee | Phase 5: Story elaboration | PENDING | Phase 3 |
+| f39af70f-72c5-4ac1-9522-83c2e11b37c9 | Phase 6: Doot — Claudomator integration | PENDING | Phase 3 |
+
+Instruction files: `scripts/.claude/phase{3,4,5,6}-*-instructions.txt`
+
+### Phase 3: Stories data model (claudomator repo)
+- `internal/task/story.go` — Story struct + ValidStoryTransition
+- `internal/storage/db.go` — stories table + story_id on tasks, CRUD + ListTasksByStory
+- `internal/api/stories.go` — story API endpoints
+- Tests: ValidStoryTransition, CRUD, depends_on auto-wire
+
+### Phase 4: Story execution and deploy (claudomator repo, depends Phase 3)
+- `internal/executor/executor.go` — checkStoryCompletion → SHIPPABLE
+- `internal/executor/container.go` — checkout story branch after clone
+- `internal/api/stories.go` — POST /api/stories/{id}/branch
+
+### Phase 5: Story elaboration (claudomator repo, depends Phase 3)
+- `internal/api/elaborate.go` — POST /api/stories/elaborate + approve
+- SeedProjects called at server startup
+
+### Phase 6: Doot — Claudomator integration (doot repo, depends Phase 3)
+- `internal/api/claudomator.go` — ClaudomatorClient
+- `internal/models/atom.go` — StoryToAtom, SourceClaudomator
+- `internal/handlers/atoms.go` — BuildUnifiedAtomList extended
+- `cmd/dashboard/main.go` — wire ClaudomatorURL config
+
+---
+
+## Key Files Changed (Phases 1-2)
+
+### Claudomator
+- `internal/task/project.go` — new Project struct
+- `internal/task/task.go` — removed Agent.ProjectDir, Agent.RepositoryURL, Agent.SkipPlanning
+- `internal/storage/db.go` — projects table migration + CRUD
+- `internal/storage/seed.go` — SeedProjects upserts claudomator + nav on startup
+- `internal/api/projects.go` — project CRUD handlers
+- `internal/api/server.go` — project routes; processResult no longer extracts changestats
+- `internal/api/deployment.go` + `task_view.go` — use tk.RepositoryURL (was tk.Agent.ProjectDir)
+- `internal/executor/container.go` — fallback logic removed; requires t.RepositoryURL
+
+### Doot
+- Bug feature removed entirely (models, handlers, store, routes, template, migration)
+- `migrations/018_drop_bugs.sql` — DROP TABLE IF EXISTS bugs
+- `internal/api/interfaces.go` — AddMealToPlanner removed from PlanToEatAPI
+- `internal/api/plantoeat.go` — AddMealToPlanner stub removed
+- `internal/models/atom.go` — SourceBug, TypeBug, TypeNote, BugToAtom removed