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Implement milestone→flow link in questio schema and tools

Goal

Add the flow field to the milestones.yml schema convention and update questio_gap to return it in structured output. Also update pixecog's milestones.yml with flow values.

Context

The loop mechanisms spec requires the agent to resolve from questio milestones to pipeio flows without free-text parsing. The flow field in milestones.yml provides this structured link.

Read the updated design spec at docs/specs/research-orchestration/design.md (section 5.2) for the schema definition, and docs/specs/research-orchestration/loop-mechanisms.md (section 4) for how orient uses it.

Prompt

Step 1: Read the specs. - Read /storage2/arash/projects/projio/docs/specs/research-orchestration/design.md section 5.2 for the milestone schema with flow field - Read /storage2/arash/projects/projio/docs/specs/research-orchestration/loop-mechanisms.md for how the flow field is used

Step 2: Update questio_gap tool in src/projio/mcp/questio.py. - When parsing milestones.yml, read the flow field - Include flow in the structured output for each milestone returned by questio_gap - If flow is not set, fall back to the first entry in pipelines list (backward compat)

Step 3: Update questio_status tool to also include the flow field in its output.

Step 4: Update pixecog's milestones.yml at /storage2/arash/projects/pixecog/plan/milestones.yml. - Add flow: field to each milestone, mapping to the correct pipeio flow name - For milestones spanning multiple flows (like preprocessing-stable), use the primary flow and keep pipelines for the full list

Step 5: Validate — run questio_status and questio_gap against pixecog to verify the flow field appears in output.

Step 6: Commit projio changes with: "Add flow field to questio milestone schema and tool output" Step 7: Commit pixecog changes with: "Add flow field to milestones.yml"

Acceptance Criteria

  • [ ] questio_gap returns flow field per milestone
  • [ ] questio_status returns flow field per milestone
  • [ ] pixecog milestones.yml has flow values for all milestones
  • [ ] Backward compatible when flow field is absent
  • [ ] Both repos committed

Batch Result

  • status: done
  • batch queue_id: d63b4b31684a
  • session: be6951d6-6bf8-4098-b8ae-20e0a01542ea
  • batch duration: 527.5s