Retire idea.md / --idea operator-seed pathway

CHANGELOG.md

@@ -5,6 +5,31 @@ All notable changes to the ACE plugin will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and the plugin follows [semantic versioning](https://semver.org/spec/v2.0.0.html).
 
+## 0.13.329 — 2026-05-22
+
+**Retire `idea.md` / `--idea` operator-seed pathway.**
+
+The 2026-05-05 refactor reduced `idea.md` to an optional `--idea FILE|-` seed alongside the `inputs/` evidence pack. The dual-path persisted but was rarely used in practice and added cognitive load: the eval rubric carried a clean-source dual-branch keyed off "idea.md contains reviewer comments," the orchestrator had a special `--idea`-was-passed scripted-seed flow at run start, `idea-to-pdd` scanned the `idea.md` body for Drive URLs in its permission pre-flight, and the artifact manifest carried two `idea.md` entries (run-root + legacy `1-design/idea.md` back-compat) with their corresponding RUN_LEVEL_EXEMPT carve-outs.
+
+Operators now put any free-text seed directly into `inputs/` as a regular source file alongside everything else. One canonical input pathway, one synthesis surface.
+
+Removed:
+- `--idea FILE|-` argument from `/ace:run`
+- The scripted-seed branch in `agents/ace-orchestrator.md § Starting a New Opportunity`
+- The "If `--idea FILE|-` was passed" sub-step at run-folder bootstrap
+- The `idea.md=<present|absent>` field from the orchestrator's start-of-run log line
+- The optional `idea.md` table row in `skills/idea-to-pdd/SKILL.md § Inputs`
+- The `idea.md`-URL extraction in `idea-to-pdd`'s pre-flight permission scan
+- The "or no idea.md" arm of the missing-source-material error
+- Both `idea.md` and `1-design/idea.md` (legacy back-compat) entries from `lib/artifact-manifest.ts`
+- The `runs/<run-id>/idea.md` row in `agents/orchestrator-reference.md § Per-run`
+- The two legacy `1-design/idea.md` fixture files under `test/fixtures/CRISPR-Test-00{1,2}/`
+
+Preserved:
+- The `clean_source` detection mechanism in `idea-to-pdd-eval` (still useful — keys off reviewer-comment presence across the source pack, not specifically `idea.md`). Dual-branch dimension scoring unchanged; language updated.
+- Historical changelog entries in `skills/idea-to-pdd/SKILL.md` and `skills/idea-to-pdd-eval/SKILL.md` (audit trail of evolution from single-`idea.md` → multi-doc evidence pack → no-`idea.md`).
+- `scripts/migrate-drive-layout.ts` `idea.md → 1-design/idea.md` mapping (back-compat tool for migrating legacy pre-2026-05-05 runs).
+
 ## 0.13.299 — 2026-05-21
 
 **`/ace:doctor` catches Nova MCP stuck-in-needs-auth-cache state.**

agents/ace-orchestrator.md

@@ -266,7 +266,6 @@ message.** Issue together:
 
 - `drive_create_folder` for `<opp>/runs/<run-id>/`
 - `drive_create_file` for `runs/<run-id>/run_state.yaml` (initial — phases all pending)
-- `drive_create_file` for `runs/<run-id>/idea.md` (only if `--idea FILE|-` was passed)
 - `drive_create_file` for `runs/<run-id>/inputs-manifest.yaml` (frozen file_id list from Step 3)
 
 **Step 6 — Dispatch Phase 1.** Single `Agent(idea-to-design)` call with
@@ -544,7 +543,6 @@ ACE/                              (= ACE_DRIVE_ROOT_FOLDER_ID)
 │   │   └── <run-id>/             (e.g. "20260502-1830")
 │   │       ├── run_state.yaml
 │   │       ├── inputs-manifest.yaml  (frozen file_id list captured at run start)
-│   │       ├── idea.md           (optional — only present when --idea FILE|- was passed)
 │   │       └── 1-design/
 │   │           ├── idea-to-pdd.md         (the formal PDD — Phase 1 output)
 │   │           └── ... (other Phase 1 outputs)
@@ -594,14 +592,7 @@ in `inputs/` (the manifest), not to pick one canonical PDD file.
    (next to `opp.yaml`) without knowing about the `inputs/` requirement.
    See jjackson/ace#299.
 
-   **(b) `--idea FILE|-` was passed**: scripted-seed flow. If `<opp>`
-   was also provided, use it; otherwise auto-generate a fresh slug
-   `smoke-<YYYYMMDD-HHMM>` (today's behavior). Write the idea body
-   directly into `runs/<run-id>/idea.md` at step 5 — this path
-   bypasses `inputs/` entirely (scripted runs are non-interactive by
-   design). No `inputs/pdd.md` write.
-
-   **(c) Zero-arg discovery** (default when neither (a) nor (b)):
+   **(b) Zero-arg discovery** (default when (a) does not apply):
 
    1. Read `ACE_DRIVE_ROOT_FOLDER_ID`. If unset/empty, error:
       `ACE_DRIVE_ROOT_FOLDER_ID is not set in your .env (expected at
@@ -652,7 +643,7 @@ in `inputs/` (the manifest), not to pick one canonical PDD file.
    folder ID; this is the **run folder ID** that gets passed to every
    downstream skill in place of the previous "opp folder ID".
 
-5. **Capture the inputs manifest and (optionally) seed `idea.md`.**
+5. **Capture the inputs manifest.**
 
    The PDD is the formal output of Phase 1, not an input. The
    orchestrator's job here is to record what was in `inputs/` at
@@ -707,21 +698,18 @@ in `inputs/` (the manifest), not to pick one canonical PDD file.
    they run (see § Per-Phase Folder Lifecycle). The orchestrator does
    NOT pre-create `1-design/` here.
 
-   **If `--idea FILE|-` was passed**, the command has loaded the body.
-   Write it verbatim to `runs/<runId>/idea.md` via `drive_create_file`
-   — this is the operator's free-text seed and stands alongside the
-   manifest as supplementary intent. `idea-to-pdd` reads both.
-
-   **Otherwise**, do NOT seed an `idea.md`. The manifest alone is
-   sufficient — `idea-to-pdd` reads each file in the manifest as the
-   evidence pack and synthesizes the PDD from there.
+   The manifest is the sole seed for Phase 1 — `idea-to-pdd` reads
+   each file in the manifest as the evidence pack and synthesizes
+   the PDD from there.
 
    The previous single-file `pdd.md` discovery (`pdd.md` exact,
    `*pdd*` glob, lone-doc fallback, multi-doc error) is removed
    entirely. There is no longer a copy of any input file into the run
    folder — `inputs/` is the canonical read-only seed pack and
    `idea-to-pdd` reads its files directly via the manifest's
-   `file_id`s.
+   `file_id`s. (The pre-2026-05-22 `--idea FILE|-` operator-seed
+   flag was also retired — operators put any free-text seed directly
+   into `inputs/` as a regular source file.)
 
 6. **Initialize `run_state.yaml`** at `<opp>/runs/<runId>/run_state.yaml` with:
    - `mode`, `created` (ISO timestamp), all steps as `pending`
@@ -781,7 +769,6 @@ in `inputs/` (the manifest), not to pick one canonical PDD file.
      inputs_folder=<opp>/inputs (read-only, <N> files in manifest)
      run_folder=<opp>/runs/<runId>
      manifest=<opp>/runs/<runId>/inputs-manifest.yaml
-     idea.md=<present|absent>   # present only when --idea FILE|- was passed
    ```
 
 9. **Begin Phase 1.**
@@ -809,9 +796,6 @@ picker.
 > already exists), and re-run `/ace:run <opp>`. Top-level drops
 > directly under `ACE/<opp>/` are also fine — the orchestrator
 > auto-migrates them into `inputs/` on next run.
->
-> Or pass `--idea FILE|-` to seed a free-text idea directly without
-> using `inputs/`.
 
 The legacy `PDD/` flat folder is kept readable by ace-web for back-compat
 viewing of legacy opps, but is no longer consulted for new runs.
@@ -824,7 +808,7 @@ When invoked with an opportunity, execute these phases in order:
 
 **Dispatch:** `Agent(idea-to-design)`.
 
-**Inputs (inline at handoff):** the inputs manifest, any `idea.md`, `run_state.yaml`. See § Pre-flight & per-phase conventions → "Pass artifacts inline at phase handoff" for the prompt template.
+**Inputs (inline at handoff):** the inputs manifest, `run_state.yaml`. See § Pre-flight & per-phase conventions → "Pass artifacts inline at phase handoff" for the prompt template.
 
 **Atoms / skills used (orchestrator-visible only):** `Agent(idea-to-design)`.
 

agents/idea-to-design.md

@@ -37,9 +37,9 @@ this subagent's steps have these read-redundancy rules:
   the PDD MAY be rewritten by Step 1.4's QA retry loop — if QA
   dispatched the producer with an `auto_fix_hint`, re-read the PDD
   after that loop terminates.
-- **Batch the Step 1 input reads.** `inputs-manifest.yaml`, each
-  manifest entry, and optional `idea.md` are independent — issue them
-  as ONE parallel `drive_read_file` block, not sequentially.
+- **Batch the Step 1 input reads.** `inputs-manifest.yaml` and each
+  manifest entry are independent — issue them as ONE parallel
+  `drive_read_file` block, not sequentially.
 - **Skill-level reads are governed by each `SKILL.md`.** This subagent
   controls only the reads it issues directly between steps; reads
   inside the producer/QA/eval skills are out of scope here.
@@ -52,8 +52,6 @@ Invoke the `idea-to-pdd` skill.
   - `ACE/<opp-name>/runs/<run-id>/inputs-manifest.yaml`
     (frozen pointer-set captured by the orchestrator from `<opp>/inputs/`)
   - Each file referenced in the manifest (read inline)
-  - Optional: `ACE/<opp-name>/runs/<run-id>/idea.md` if `--idea FILE|-`
-    was passed (operator free-text seed; stands alongside the manifest)
 - Output: `ACE/<opp-name>/runs/<run-id>/1-design/idea-to-pdd.md`
   (the formal PDD — Phase 1's primary artifact)
 - **Gate (review mode):** Present the PDD for approval before continuing
@@ -72,9 +70,8 @@ Invoke the `idea-to-pdd-qa` skill — runs 6 static structural checks against th
 ### Step 1.5: Idea-to-PDD eval (independent quality re-grade)
 Unless `--no-evals` was passed AND QA verdict is `pass`, invoke the `idea-to-pdd-eval` skill.
 - Inputs: the same source material `idea-to-pdd` consumed
-  (`inputs-manifest.yaml` + each manifest entry, plus run-root
-  `idea.md` if present) + the produced PDD at
-  `ACE/<opp-name>/runs/<run-id>/1-design/idea-to-pdd.md`
+  (`inputs-manifest.yaml` + each manifest entry) + the produced PDD
+  at `ACE/<opp-name>/runs/<run-id>/1-design/idea-to-pdd.md`
   **(all in subagent context from Step 1 / Step 1.4 — do NOT re-read)**
 - Output: `ACE/<opp-name>/runs/<run-id>/1-design/idea-to-pdd-eval_verdict.yaml` (machine-readable
   verdict in the shared shape — see `skills/README.md § QA vs Eval`)

agents/orchestrator-reference.md

@@ -374,7 +374,6 @@ forking:**
 | `runs/<run-id>/run_state.yaml` | Lifecycle state — phase/step pointer, mode, `last_actor`, timestamps. New file at each new run-id. |
 | `runs/<run-id>/README.md` | Per-run index regenerated after each phase via `generateRunReadme(...)`. |
 | `runs/<run-id>/inputs-manifest.yaml` | Frozen pointer-set captured at run start (`inputs/` file_ids). Snapshots that run's view of the source pack. |
-| `runs/<run-id>/idea.md` | Optional `--idea` seed, only when `/ace:run --idea FILE\|-` was used. |
 | `runs/<run-id>/<N>-<phase>/<producer>.md` | Producer artifacts (PDDs, app summaries, training docs, screenshots, etc.). |
 | `runs/<run-id>/<N>-<phase>/<producer>_verdict[-<mode>].yaml` | Producer self-evaluation (when the producing skill self-evaluates). |
 | `runs/<run-id>/<N>-<phase>/<producer>-eval_verdict[-<mode>].yaml` | Eval-side judgment from the matching `*-eval` skill. |

commands/run.md

@@ -1,6 +1,6 @@
 ---
 description: Run the full CRISPR-Connect lifecycle for an opportunity
-argument-hint: [<opp>[/<run-id>]] [--mode default|review|auto] [--idea FILE|-] [--ace-web-url URL] [--dry-run] [--sandbox] [--no-evals]
+argument-hint: [<opp>[/<run-id>]] [--mode default|review|auto] [--ace-web-url URL] [--dry-run] [--sandbox] [--no-evals]
 allowed-tools: [Read, Write, Edit, Bash, Glob, Grep, Agent, AskUserQuestion]
 ---
 
@@ -34,12 +34,6 @@ Run the full CRISPR-Connect lifecycle for a Connect opportunity.
     approval. Use for high-touch operations or training.
   - `auto` — never pause for any gate. For unattended batch runs
     (e.g. eval calibration). `[BLOCKER]` concerns still escalate.
-- `--idea FILE|-` — pre-seed a free-text `idea.md` from a file path, or `-`
-  for stdin. Operator-supplied seed; stands alongside the inputs/
-  evidence-pack manifest as supplementary intent. Content is uploaded
-  verbatim to `ACE/<opp>/runs/<run-id>/idea.md` via `drive_create_file`.
-  Most runs do not need this flag — the inputs/ evidence pack alone is
-  sufficient seed material for `idea-to-pdd`.
 - `--ace-web-url URL` — after the orchestrator completes, invoke the
   `upload-transcript` skill to POST the run's stream-json transcript to
   `<URL>/api/ingest/upload`. **Smart default:** if this flag is omitted
@@ -89,21 +83,18 @@ seed material for the PDD; there is no required filename.
 
 Resolution:
 
-1. If `--idea FILE|-` was passed, scripted-seed flow: write the idea
-   body to `runs/<run-id>/idea.md` directly (operator free-text seed).
-   Manifest capture still runs from `inputs/` if it exists.
-2. Else read `ACE_DRIVE_ROOT_FOLDER_ID`. Stop with an actionable error
+1. Read `ACE_DRIVE_ROOT_FOLDER_ID`. Stop with an actionable error
    if unset.
-3. List `ACE/`. Find subfolders containing an `inputs/` subfolder.
-4. Pick the candidate with the newest `inputs/` mtime; folder name = `<opp>`.
-5. If no candidate exists, stop with the new-layout setup message.
-6. Generate `runId` = `YYYYMMDD-HHMM` (collision-suffixed).
-7. `mkdir <opp>/runs/<runId>/`; capture
+2. List `ACE/`. Find subfolders containing an `inputs/` subfolder.
+3. Pick the candidate with the newest `inputs/` mtime; folder name = `<opp>`.
+4. If no candidate exists, stop with the new-layout setup message.
+5. Generate `runId` = `YYYYMMDD-HHMM` (collision-suffixed).
+6. `mkdir <opp>/runs/<runId>/`; capture
    `runs/<runId>/inputs-manifest.yaml` (frozen pointer-set of every
    direct child file under `inputs/`). No input file is copied — the
    PDD is synthesized at Phase 1 from the manifest.
-8. Init `run_state.yaml`; update `opp.yaml.last_run_id`.
-9. Begin Phase 1.
+7. Init `run_state.yaml`; update `opp.yaml.last_run_id`.
+8. Begin Phase 1.
 
 See `agents/ace-orchestrator.md` for full detail.
 
@@ -124,12 +115,6 @@ See `agents/ace-orchestrator.md` for full detail.
      tell the operator "defaulting --ace-web-url to labs".
    - Otherwise, leave unset (skip the post-run upload hook).
 
-1b. If `--idea` was provided, read its body:
-   - If the value is `-`, read stdin until EOF.
-   - Otherwise treat the value as a file path; read its bytes as UTF-8.
-   Pass the body through to the orchestrator alongside the slug so the
-   "Starting a New Opportunity" flow can skip its PDD-picker.
-
 2. **Execute the orchestration procedure inline at top-level.** Read
    `agents/ace-orchestrator.md` and follow it as a procedure document
    from this (top-level) Claude Code session. Do **not** dispatch
@@ -143,7 +128,6 @@ See `agents/ace-orchestrator.md` for full detail.
    Inputs to thread through:
    - Slug
    - Execution mode
-   - Idea body (if `--idea` was provided)
    - Dry-run flag (if set)
    - Sandbox flag (if set)
    - Any existing state from GDrive (if resuming)

commands/step.md

@@ -92,8 +92,8 @@ Implementation steps the agent (or a thin Bash wrapper) must perform:
      `inputs/`, `eval-calibration/known-issues.md`) resolve to
      `ACE/<opp>/<path>`. Run-scoped entries (anything under
      `1-design/`, `2-scenarios/`, … `8-execution/`, plus
-     `run_state.yaml`, `inputs-manifest.yaml`, `idea.md`,
-     `decisions.yaml`) resolve to `ACE/<opp>/runs/<runId>/<path>`.
+     `run_state.yaml`, `inputs-manifest.yaml`, `decisions.yaml`)
+     resolve to `ACE/<opp>/runs/<runId>/<path>`.
    - Use `drive_list_folder` (or the live Drive listing) to check that
      the resolved path exists.
 3. If any required artifact is missing, print an error of the form:
@@ -137,8 +137,8 @@ skills in dependency order) still enforces the contract.
 ```text
 /ace:step idea-to-pdd my-opp
   → Bare opp. Resolves runId from opp.yaml.last_run_id.
-  → Reads ACE/my-opp/runs/<last_run_id>/inputs/idea.md (required,
-    producedBy: external). OK → invoke skill.
+  → Required: inputs-manifest.yaml at the run root (produced by
+    ace-orchestrator at run start). OK → invoke skill.
 
 /ace:step app-screenshot-capture malaria-itn-app/20260517-1829
   → Pinned run-id. Targets ACE/malaria-itn-app/runs/20260517-1829/

lib/artifact-manifest.ts

@@ -144,22 +144,6 @@ export const ARTIFACT_MANIFEST: readonly ArtifactEntry[] = [
     required: false,
     description: 'Frozen pointer-set captured at run start: every direct child file under inputs/ as {file_id, name, mime_type}. idea-to-pdd reads each entry to synthesize the PDD. Lives at the run-folder root alongside run_state.yaml — both are run-level metadata, scoped beyond any single phase. Pointing at file_ids (not paths) means a human re-arranging inputs/ mid-run does not shift the source pack out from under Phase 1. NOT YET required: existing fixtures predate the 2026-05-05 evidence-pack refactor; flip to required=true once the next round of fixture updates lands.',
   },
-  {
-    path: 'idea.md',
-    producedBy: 'external',
-    consumedBy: ['idea-to-pdd'],
-    phase: 'design',
-    required: false,
-    description: 'Optional operator-supplied free-text seed at the run-folder root. Only present when /ace:run was invoked with --idea FILE|-. Read by idea-to-pdd alongside the inputs-manifest. Most runs do not have this file — the inputs/ evidence pack is sufficient.',
-  },
-  {
-    path: '1-design/idea.md',
-    producedBy: 'external',
-    consumedBy: ['idea-to-pdd'],
-    phase: 'design',
-    required: false,
-    description: 'Legacy path — pre-2026-05-05 the orchestrator copied inputs/pdd.md into 1-design/idea.md as the seed for idea-to-pdd. New runs do not write this file (the manifest at 1-design/inputs-manifest.yaml replaces it; --idea seeds the run-root idea.md). Kept in the manifest so older fixtures and resumed legacy runs validate cleanly.',
-  },
   {
     path: '1-design/idea-to-pdd.md',
     producedBy: 'idea-to-pdd',

mcp/google-drive-server.ts

@@ -143,8 +143,8 @@ function error(msg: string) {
  *
  * Inflight-dedupe + 30s TTL cache (added 2026-05-10, perf lens). When N
  * parallel writes target the same parent — common for run-folder bootstrap
- * (run_state.yaml + idea.md + inputs-manifest.yaml + gate-brief.md often go
- * into the same `runs/<run-id>/` parent in one batched message) — the first
+ * (run_state.yaml + inputs-manifest.yaml often go into the same
+ * `runs/<run-id>/` parent in one batched message) — the first
  * caller's probe populates the inflight slot; concurrent callers await the
  * same promise instead of firing N redundant `files.get` round-trips. After
  * the probe resolves, an `ok: true` result is cached for 30s so a follow-up