Explicit optional-organ setup and pause states

Type: feature
Epic: scientist-adoption-pilot
Target: PyAutoScientist
Difficulty: medium
Autonomy: supervised
Consequence: judge
Status: proposed

Original request

ok conitnue

Context and scope

Continue the optional-organ activation milestone after Broca setup and publication
PRs #17/#19. @PyAutoScientist currently stores only connected organs and fetches
every selected feed. Add explicit setup and observation-pause state, while owners
retain readiness and jobs. This is one Scientist PR, not remote provisioning.

High-level plan

• Show available organs and setup-incomplete entries without contacting their feeds.
• Keep connected, paused and evidence-needs-attention states distinct.
• Add preview/apply operations to begin setup, pause observation and validate resume.
• Prove transitions, preservation and zero fetches for setup/paused organs in Python
  and browser checks; document the fresh-chat workflow.

Tier: judge — merge mode: human /prm.

Detailed implementation plan

1. scripts/instance_profile.py: extend schema v1 compatibly with optional
   organ_setup entries (canonical organ key -> explicit repo/pages_url) and an
   optional boolean paused on existing connections. Existing profiles remain
   valid and unchanged by loading. Reject an organ appearing in both maps. No
   local setup paths, task history or private records enter public snapshots.
2. scripts/organ_lifecycle.py (new): preview/apply begin-setup and pause/resume
   actions; reuse existing profile/project validation and atomic input-checked
   writes. Store only chosen connection/setup state; Mind remains the task ledger.
   Resume validates the selected HTTPS feed and identity before unpausing.
3. scripts/connect_organ.py: promote a matching pending setup entry only after
   successful feed validation. Preserve no-op/retry behavior, reject conflicting
   identities, and require explicit resume for a paused connection. Never discard
   configured connection data when the feed becomes unavailable.
4. scripts/organism_board.py and scripts/overview.js: render an opt-in available
   catalogue plus setup-incomplete and paused cards for independent profiles.
   Skip setup/paused feed requests on server and browser, including startup,
   interval and visibility refresh; do not revive cached evidence as current.
   Keep connected evidence status separate from configuration state. Use existing
   shared components and native disclosures; preserve keyboard focus and no-JS
   readability. Available/setup entries are not counted as connected or included
   as active board destinations. Existing unprofiled dashboard behavior is retained.
5. Extend profile, connection, collector and Node/browser tests: old-profile
   compatibility; invalid transitions; failed validation preserves profile bytes;
   setup->connected->paused->resumed; changed-input refusal; no network while
   pending or paused; grey/stale/missing feeds never imply an uninstalled organ;
   browser/server agreement and cache behavior. Inspect representative desktop
   and mobile rendering with a differently named instance.
6. STARTER.md and a bounded example: distinguish pause of Scientist observation
   from stopping jobs/services. Explain availability, setup, validated connection,
   pause and owner evidence. Use copyable AI prompts, not browser-side config writes.

Acceptance boundaries

Pause means Scientist observation only. It does not cancel compute, suspend GitHub
Actions or stop services. Connection means validated location/contract, not healthy
evidence. No hosting destination or collaborator access is needed for this PR.
Live independent deployment, record-preserving upgrades and collaborator validation
remain separate milestones.

Branch and readiness survey

Scientist canonical main is clean at 2f69a3a; no active claim. An old unregistered
pyautodna-stack-management worktree is clean with no commits ahead of main and
will be left alone. Proposed branch feature/scientist-organ-lifecycle, bundle
.worktrees/scientist-organ-lifecycle; start_workspace -> ship_workspace.

Three clean canonical library checkouts were fast-forwarded to resolve Heart's
behind-origin reasons. Refreshed Heart at 2026-10-12T14:30:53Z: STALE, no RED or
YELLOW reasons; only release validation incomplete: no rehearsal for current source.
This permits development, not release. Plan awaits explicit approval.