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-**`EDIT`**: Modifying specific sections of existing drafts.
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2.**Constraint Identification**: Parse the user's prompt for all explicit constraints (e.g., target filenames, section length requirements like "occupy 85% of character limits", number of review rounds, specific funder guidelines).
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3.**Initial State Check**: If the intent is `REGENERATE` or `EDIT`, verify that the specified target files exist within the project. If not, ask the user for the correct path or confirm a switch to `CREATE_NEW` mode.
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4.**Plan Generation**: Create a step-by-step execution plan in Markdown. The plan must list each phase, the actions to be taken, the target files, and the identified constraints.
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5.**Confirmation Gate**: Present the plan to the user. Halt execution until the user explicitly approves the plan (e.g., with "Approved", "Proceed", "Yes").
> **This phase is non-negotiable. Drafting MUST NOT begin until all cited references are available locally.**
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1.**Inventory**: Scan `<PROJECT_ROOT>/.wiki/` and `00.RawData/Literature/03_Parsed_Markdown/` to identify all currently ingested papers.
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2.**Gap Detection**: Cross-reference the project's bibliography (e.g., `References/` folder, `.wiki/entities/`, or a user-provided DOI list) against ingested papers. Identify any DOIs/PMIDs that are referenced but NOT yet downloaded.
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3.**Auto-Retrieval**: If gaps are found, trigger `/literature-ingest` with the missing identifiers and wait for completion before proceeding. (Ensure you pass `--base-dir <PROJECT_ROOT>` to route artifacts locally per the Universal PDF Processing Mandate).
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4.**Retraction Scan**: Run `retraction-watcher` on the full reference list. Any retracted citation triggers a **mandatory HALT** — inform the PI and require a replacement citation before continuing.
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5.**Verification Gate**: Confirm that ALL key cited papers exist in both `03_Parsed_Markdown/`(for LLM context) and `04_Parsed_JSON/` (for structural validation). If any remain missing after retrieval, notify the PI and proceed only with available evidence, flagging missing citations explicitly.
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1.**Inventory**: Scan `./.wiki/` and `00.RawData/Literature/03_Parsed_Markdown/` to identify all currently ingested papers.
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2.**Gap Detection**: Cross-reference the project's bibliography against ingested papers. Identify any DOIs/PMIDs that are referenced but NOT yet downloaded.
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3.**Auto-Retrieval**: If gaps are found, trigger `/literature-ingest` with the missing identifiers and wait for completion.
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4.**Retraction Scan**: Run `retraction-watcher` on the full reference list. Any retracted citation triggers a **mandatory HALT** — inform the PI and require a replacement citation before continuing.
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5.**Verification Gate**: Confirm that ALL key cited papers exist in both `03_Parsed_Markdown/` and `04_Parsed_JSON/`. If any remain missing, notify the PI and proceed only with available evidence, flagging missing citations explicitly.
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## Phase 1: Intake & Funder Configuration
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1.**Scouting (Optional):** If the funder is unknown, use `grant-funding-scout` and `scientific-brainstorming` to identify a target agency.
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2.**Profile Lookup:** Search the`grant_funder_profiles` KI for an existing profile: `read_ki_document(ki_name="grant_funder_profiles", document_path="artifacts/<funder_id>.json")`.
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3.**Profile Generation (Fallback):** If no profile exists and the user provides a PDF/URL of the call, use the `pdf-extract-experimental-materials`skill to extract constraints and generate a new `funder_profile.json`→ save it to the KI artifacts directory.
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1.**Scouting (Optional):** If the funder is unknown, use `grant-funding-scout` and `scientific-brainstorming` to identify a target agency.
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2.**Profile Lookup:** Search `grant_funder_profiles` KI for an existing profile: `read_ki_document(ki_name="grant_funder_profiles", document_path="artifacts/<funder_id>.json")`.
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3.**Profile Generation (Fallback):** If no profile exists, use `pdf-extract-experimental-materials`on a user-provided PDF/URL to generate a new `funder_profile.json`and save it.
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-*Logic Gap Prevention:* If PDF extraction fails, do NOT halt. Fallback to interactive chat: ask the PI for section names, limits, and budget rules manually.
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4.**Knowledge Consolidation:** Run `knowledge-consolidation` to synthesize researcher ORCID/researchmap data and wiki context.
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5.**Confirmation:** Stop and request user confirmation of the Funder Profile and core project data.
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4.**Knowledge Consolidation:** Run `knowledge-consolidation` to synthesize researcher data and wiki context.
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## Phase 2: Visual Scheme & Timeline Generation
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1.**Workflow Diagram**: Use `visualize-data` to generate a high-resolution SVG/PNG technical workflow diagram based on the research plan, utilizing `fireworks-tech-graph` templates (per `agentic_diagramming_standard` KI). Choose the appropriate visual style from the 7 available options (e.g., `style-4-notion-clean` for grant proposals, `style-1-flat-icon` for journal figures).
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2.**Gantt / Milestone Timeline**: If the funder profile requires milestones, use `visualize-data` with the Gantt chart or grant lifecycle domain templates to create a timeline visualization.
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1.**Workflow Diagram**: Use `visualize-data` to generate a technical workflow diagram (SVG/PNG) based on the research plan, adhering to the `agentic_diagramming_standard` KI.
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2.**Gantt / Milestone Timeline**: If required, use `visualize-data` with Gantt chart templates to create a timeline visualization.
1.**Scaffold:** Parse the sections defined in `funder_profile.json.sections`. Use `research-proposal-generator` to scaffold initial evidence limits in `00.Projects/<ProjectName>/GrantDraftElements/`.
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2.**Drafting (Anti-Truncation):** Iteratively draft each section as a **separate LLM call**. *Strictly adhere to the `output-truncation-management` policy.*
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3.**Citation-Before-Claim Protocol (MANDATORY):** Before writing any evidence-based claim, run `/wiki-query` or `literature-close-read` on the relevant ingested paper. Use the scratchpad pattern:
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```
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GROUNDING CHECK:
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Claim: "[The proposed claim text]"
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Source: "[Exact quote from .wiki/ or 03_Parsed_Markdown/]"
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File: [path/to/source.md or [[wiki-page]]]
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Verdict: GROUNDED / NOT_FOUND
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```
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If `NOT_FOUND`, run `/wiki-research` or flag as `[UNGROUNDED]`. **Do NOT write the claim until it is GROUNDED.**
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4.**Translation:** If `funder_profile.languages` includes multiple languages (e.g., `["en", "ja"]`), write ALL English files first, then invoke `medical-translation` to generate localized equivalents.
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5.**Compression:** If a section has a `limit_type` (chars/words/pages), invoke `abstract-trimmer`.
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-*Dead-End Prevention:* Generate 2-3 compression variants. If the agent cannot compress it to fit, halt and ask the PI to choose a variant or manually edit.
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> **Actor Persona:**`manuscript_writer`
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1.**Scaffold:** Parse `funder_profile.json.sections`. Use `research-proposal-generator` to scaffold initial Markdown files in `./GrantDraftElements/`.
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2.**Drafting (Anti-Truncation):** Iteratively draft each section as a **separate LLM call**. *Strictly adhere to the `output-truncation-management` policy.*
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3.**Draft, Placeholder, and Ground Protocol (MANDATORY):**
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a. **Draft First**: Write a full paragraph or section focusing on scientific flow and argumentation.
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b. **Insert Placeholders**: After drafting, review the text and insert citation placeholders for every evidence-based claim, e.g., `[CITE: mechanism of action for drug X]`.
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c. **Grounding Pass**: In a separate, dedicated step, use `/wiki-query` or `literature-close-read` to resolve all `[CITE: ...]` placeholders with actual references. Any claim that cannot be grounded must be flagged as `[UNGROUNDED - EVIDENCE REQUIRED]`.
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4.**Content Length Adjustment**:
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-**Expansion**: If the Phase 0 plan includes a minimum length constraint (e.g., "85% fill rate"), and a drafted section is too short, invoke the `content-expander` skill to elaborate on technical details, add context, or provide more examples.
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-**Compression**: If a section exceeds a `limit_type` (chars/words), invoke `abstract-trimmer`.
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-*Dead-End Prevention:* If automated adjustments fail to meet constraints, halt and ask the PI for guidance.
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5.**Translation:** If `funder_profile.languages` requires multiple languages, write ALL English files first, then invoke `medical-translation` to generate localized equivalents.
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## Phase 4: CV, Publications & Budget Generation
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1.**Biosketch/CV:** If `funder_profile` requires a CV, generate it using `academic-cv-generator`.
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2.**Budget:** Run `grant-budget-justification` against `funder_profile.budget` constraints (caps, indirect rates, personnel limits).
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1.**Biosketch/CV:** If required, generate using `academic-cv-generator`.
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2.**Budget:** Run `grant-budget-justification` against `funder_profile.budget` constraints.
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## Phase 5: Simulated Peer Review & Quality Gates
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> **Minimum 3 review rounds are MANDATORY regardless of initial score.**
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> **Actor Persona:**`peer_reviewer`
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1.**Mock Review (≥3 Rounds):** Run `grant-mock-reviewer` (Actor-Critic pattern from `agentic_manuscript_publishing` KI) to assess the draft against `funder_profile.evaluation_criteria`.
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- Output each review round as a new `## Round N` section in `<ProjectRoot>/GrantDraftElements/REVIEW_LOG.md`.
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-**Grounding Audit:** The reviewer MUST flag any claim that cannot be traced to a `.wiki/` or `03_Parsed_Markdown/` source as `[UNGROUNDED — CITE REQUIRED]`.
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1.**Review Round Configuration**:
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-**Default:** Minimum of 3, maximum of 5 refinement rounds.
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-**User Override:** If the user specified a number of rounds in the initial prompt (and it was approved in the Phase 0 plan), that number becomes the **mandatory** target.
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2.**Mock Review Loop:** Run `grant-mock-reviewer` to assess the draft against `funder_profile.evaluation_criteria`.
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- Output each review round as a new `## Round N` section in `./GrantDraftElements/REVIEW_LOG.md`.
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-**Grounding Audit:** Reviewer MUST flag any claim not backed by a citation as `[UNGROUNDED — CITE REQUIRED]`.
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-**Retraction Audit:** Verify the final reference list with `retraction-watcher` after every revision round.
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-*Loop Enforcement:* Run a minimum of **3 refinement rounds**. Even if the draft passes evaluation criteria before Round 3, continue with a "hardening review" targeting citation completeness, budget accuracy, and language compliance. Maximum 5 rounds total (per `gepa_protocol`). If it still fails after Round 5, escalate to the PI.
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2.**Quality Gates:**Run `content-proofreading`, `semantic-consistency-auditor`, and `response-relevance` to verify grammar, cross-section coherence, and mandate compliance.
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-**Loop Enforcement:** Continue review/refinement cycles until the target number of rounds is complete. If the draft fails evaluation after the final round, escalate to the PI.
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3.**Quality Gates:**After the final review round, run `content-proofreading`, `semantic-consistency-auditor`, and `response-relevance`.
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## Phase 6: Assembly, Finalization & Delivery
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1.**Assembly:** Compile sections per the `submission_format` constraint (e.g., inject into `.xlsx`, use Pandoc for PDF/LaTeX, or `word-read-write` for `.docx`). *Enforce `markdown_first_manuscript_policy`.*
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2.**Interactive HTML Report (Optional):** If the PI requests an interactive deliverable or a shareable progress report, run the `md-html-docx-generator` skill on the assembled Markdown:
3.**Oral Defense:** If `has_oral_defense` is true, invoke `q-and-a-prep-partner` to generate an elevator pitch and defense material.
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4.**Secure Delivery:** If requested by the PI, invoke `secure-html-delivery` to encrypt the HTML deliverables for external sharing via AES-256-GCM.
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5.**Commit:** Execute `/lab-commit` to transactionally save the state to version control.
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1.**Assembly:** Compile sections per the `submission_format` constraint (e.g., inject into `.xlsx`, use Pandoc for PDF/LaTeX, or `word-read-write` for `.docx`). *Enforce `markdown_first_manuscript_policy`.*
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2.**Interactive HTML Report (Optional):** If requested, run `md-html-docx-generator`.
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3.**Oral Defense:** If `has_oral_defense` is true, invoke `q-and-a-prep-partner`.
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4.**Secure Delivery:** If requested, invoke `secure-html-delivery` to encrypt HTML deliverables.
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5.**Commit:** Execute `/lab-commit` to transactionally save the state to version control.
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@@ -133,6 +133,16 @@ Run the following python script via the terminal. It checks the DB lock internal
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python3 -c "import sys; import os; sys.path.insert(0, os.path.expanduser('~/.gemini/antigravity/antigravity-evolution/src')); from antigravity_evolution.policy_evolver import propose_policy_update; from antigravity_evolution.policy_analyst import generate_performance_report; report = generate_performance_report(); propose_policy_update(report) if 'error' not in report and report.get('status') != 'insufficient_data' else print('No evolution required: ' + str(report))"
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```
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## Step 4.6: Daemon Health Verification
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Ensure that the core AROS background daemons (including the `mutation_sweeper` and `dreamer`) are executing properly without silent failures.
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```bash
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# // turbo
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python3 -c "import os, sqlite3, time; db_path = os.environ.get('BRAIN_DB_PATH', os.path.expanduser('~/.gemini/antigravity/brain.db')); db = sqlite3.connect(db_path); failed_jobs = db.execute(\"SELECT id, agent_role, created_at, status FROM swarm_jobs WHERE status = 'failed' AND created_at > datetime('now', '-24 hours')\").fetchall(); print(f'\\n=== Daemon Health Report ===\\nFailed Jobs (Last 24h): {len(failed_jobs)}'); [print(f'- {j[1]} (ID: {j[0]}) at {j[2]}') for j in failed_jobs]; db.close()"
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```
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If this health report shows recent failures for system daemons, check the SwarmDoctor logs in `~/.gemini/antigravity/logs/` to verify auto-healing was engaged.
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## Step 5: Auto-Commit
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Delegate to the canonical `/lab-commit` workflow. Do NOT write inline `git add` / `git commit` commands here — the lab-commit workflow handles staging, Obsidian symlink verification, project registry updates (e.g., INDEX.csv or PIPELINE_REGISTRY.md), and commit message formatting automatically.
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