@researai/deepscientist 1.5.16 → 1.6.0

package/src/ui/dist/assets/{project-sync-CsX08Qno.js → project-sync-DPmWKmKD.js}

@@ -1 +1 @@
-import{z as k,D as u,G as p}from"./index-Gbl53BNp.js";function y(r){if(r instanceof Error)return r.message;if(typeof r=="string")return r;try{return JSON.stringify(r)}catch{return String(r)}}class j{spaceType="workspace";projectId;authMode;docKind;socket;releaseSocket;joined=!1;joinedDocs=new Set;constructor(e,s={}){this.projectId=e,this.authMode=s.authMode??"user",this.docKind=s.docKind;const{socket:t,release:o}=k({authMode:this.authMode});this.socket=t,this.releaseSocket=o}async waitForConnected(e){this.socket.connected||await new Promise((s,t)=>{const o=window.setTimeout(()=>{a(),t(new Error("WebSocket connection timeout"))},e),c=()=>{a(),s()},i=n=>{a(),t(new Error(y(n)||"WebSocket connection error"))},a=()=>{window.clearTimeout(o),this.socket.off("connect",c),this.socket.off("connect_error",i),this.socket.off?.("error",i)},h=(n,w)=>{const d=this.socket;if(typeof d.once=="function"){d.once(n,w);return}const f=(...m)=>{typeof d.off=="function"&&d.off(n,f),w(...m)};d.on?.(n,f)};h("connect",c),h("connect_error",i),h("error",i)})}async emitWithAck(e,s,t=1e4){await this.waitForConnected(t);try{const o=this.socket;return typeof o.timeout=="function"&&typeof o.emitWithAck=="function"?await o.timeout(t).emitWithAck(e,s):await new Promise(c=>{const i=window.setTimeout(()=>{c({error:{name:"SOCKET_TIMEOUT",message:`Ack timeout for ${e}`}})},t);this.socket.emit(e,s,a=>{window.clearTimeout(i),c(a)})})}catch(o){return{error:{name:"SOCKET_ERROR",message:y(o)}}}}async connect(){if(this.joined)return;const e=await this.emitWithAck("space:join",{spaceType:this.spaceType,spaceId:this.projectId,clientVersion:"1.0.0"},12e3);if("error"in e)throw new Error(e.error.message);if(!e.data.success)throw new Error("Failed to join space");this.joined=!0}async joinDoc(e){if(!e||(this.joined||await this.connect(),this.joinedDocs.has(e)))return;const s=await this.emitWithAck("space:join-doc",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind},12e3);if("error"in s)throw new Error(s.error.message);if(!s.data.success)throw new Error("Failed to join doc");this.joinedDocs.add(e)}leaveDoc(e){e&&this.joinedDocs.has(e)&&(this.socket.emit("space:leave-doc",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind}),this.joinedDocs.delete(e))}disconnect(){try{if(this.joined){for(const e of Array.from(this.joinedDocs))this.leaveDoc(e);this.socket.emit("space:leave",{spaceType:this.spaceType,spaceId:this.projectId})}}finally{this.joined=!1,this.releaseSocket()}}onDocUpdate(e){const s=t=>{t?.spaceId===this.projectId&&e({docId:String(t.docId),update:p(String(t.update)),timestamp:Number(t.timestamp),editor:t.editor?String(t.editor):void 0})};return this.socket.on("space:broadcast-doc-update",s),()=>this.socket.off("space:broadcast-doc-update",s)}onDocReset(e){const s=t=>{t?.spaceId===this.projectId&&e({docId:String(t.docId),timestamp:Number(t.timestamp),reason:t?.reason?String(t.reason):void 0,actorUserId:t?.actorUserId!=null?String(t.actorUserId):null})};return this.socket.on("space:doc-reset",s),()=>this.socket.off("space:doc-reset",s)}async loadDoc(e,s){await this.joinDoc(e);const t=await this.emitWithAck("space:load-doc",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,stateVector:s?await u(s):void 0},15e3);if("error"in t){if(t.error.name==="DOC_NOT_FOUND"||t.error.name==="NOT_FOUND")return null;throw new Error(t.error.message)}return{missing:p(t.data.missing),state:p(t.data.state),timestamp:Number(t.data.timestamp)}}async pushDocUpdate(e,s){await this.joinDoc(e);const t=await this.emitWithAck("space:push-doc-update",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,update:await u(s)},15e3);if("error"in t)throw new Error(t.error.message);return Number(t.data.timestamp)}async joinAwareness(e){const s=await this.emitWithAck("space:join-awareness",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,clientVersion:"1.0.0"},12e3);if("error"in s)throw new Error(s.error.message);if(!s.data.success)throw new Error("Failed to join awareness")}leaveAwareness(e){this.socket.emit("space:leave-awareness",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind})}onAwarenessCollect(e,s){const t=o=>{o?.spaceId===this.projectId&&String(o?.docId)===e&&s()};return this.socket.on("space:collect-awareness",t),()=>this.socket.off("space:collect-awareness",t)}onAwarenessUpdate(e,s){const t=o=>{o?.spaceId===this.projectId&&String(o?.docId)===e&&s(p(String(o.awarenessUpdate)))};return this.socket.on("space:broadcast-awareness-update",t),()=>this.socket.off("space:broadcast-awareness-update",t)}async broadcastAwareness(e,s){this.socket.emit("space:update-awareness",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,awarenessUpdate:await u(s)})}requestAwarenesses(e){this.socket.emit("space:load-awarenesses",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind})}}export{j as P};
+import{v as k,w as u,x as p}from"./index-CHzJ2xtB.js";function y(r){if(r instanceof Error)return r.message;if(typeof r=="string")return r;try{return JSON.stringify(r)}catch{return String(r)}}class j{spaceType="workspace";projectId;authMode;docKind;socket;releaseSocket;joined=!1;joinedDocs=new Set;constructor(e,s={}){this.projectId=e,this.authMode=s.authMode??"user",this.docKind=s.docKind;const{socket:t,release:o}=k({authMode:this.authMode});this.socket=t,this.releaseSocket=o}async waitForConnected(e){this.socket.connected||await new Promise((s,t)=>{const o=window.setTimeout(()=>{a(),t(new Error("WebSocket connection timeout"))},e),c=()=>{a(),s()},i=n=>{a(),t(new Error(y(n)||"WebSocket connection error"))},a=()=>{window.clearTimeout(o),this.socket.off("connect",c),this.socket.off("connect_error",i),this.socket.off?.("error",i)},h=(n,w)=>{const d=this.socket;if(typeof d.once=="function"){d.once(n,w);return}const f=(...m)=>{typeof d.off=="function"&&d.off(n,f),w(...m)};d.on?.(n,f)};h("connect",c),h("connect_error",i),h("error",i)})}async emitWithAck(e,s,t=1e4){await this.waitForConnected(t);try{const o=this.socket;return typeof o.timeout=="function"&&typeof o.emitWithAck=="function"?await o.timeout(t).emitWithAck(e,s):await new Promise(c=>{const i=window.setTimeout(()=>{c({error:{name:"SOCKET_TIMEOUT",message:`Ack timeout for ${e}`}})},t);this.socket.emit(e,s,a=>{window.clearTimeout(i),c(a)})})}catch(o){return{error:{name:"SOCKET_ERROR",message:y(o)}}}}async connect(){if(this.joined)return;const e=await this.emitWithAck("space:join",{spaceType:this.spaceType,spaceId:this.projectId,clientVersion:"1.0.0"},12e3);if("error"in e)throw new Error(e.error.message);if(!e.data.success)throw new Error("Failed to join space");this.joined=!0}async joinDoc(e){if(!e||(this.joined||await this.connect(),this.joinedDocs.has(e)))return;const s=await this.emitWithAck("space:join-doc",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind},12e3);if("error"in s)throw new Error(s.error.message);if(!s.data.success)throw new Error("Failed to join doc");this.joinedDocs.add(e)}leaveDoc(e){e&&this.joinedDocs.has(e)&&(this.socket.emit("space:leave-doc",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind}),this.joinedDocs.delete(e))}disconnect(){try{if(this.joined){for(const e of Array.from(this.joinedDocs))this.leaveDoc(e);this.socket.emit("space:leave",{spaceType:this.spaceType,spaceId:this.projectId})}}finally{this.joined=!1,this.releaseSocket()}}onDocUpdate(e){const s=t=>{t?.spaceId===this.projectId&&e({docId:String(t.docId),update:p(String(t.update)),timestamp:Number(t.timestamp),editor:t.editor?String(t.editor):void 0})};return this.socket.on("space:broadcast-doc-update",s),()=>this.socket.off("space:broadcast-doc-update",s)}onDocReset(e){const s=t=>{t?.spaceId===this.projectId&&e({docId:String(t.docId),timestamp:Number(t.timestamp),reason:t?.reason?String(t.reason):void 0,actorUserId:t?.actorUserId!=null?String(t.actorUserId):null})};return this.socket.on("space:doc-reset",s),()=>this.socket.off("space:doc-reset",s)}async loadDoc(e,s){await this.joinDoc(e);const t=await this.emitWithAck("space:load-doc",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,stateVector:s?await u(s):void 0},15e3);if("error"in t){if(t.error.name==="DOC_NOT_FOUND"||t.error.name==="NOT_FOUND")return null;throw new Error(t.error.message)}return{missing:p(t.data.missing),state:p(t.data.state),timestamp:Number(t.data.timestamp)}}async pushDocUpdate(e,s){await this.joinDoc(e);const t=await this.emitWithAck("space:push-doc-update",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,update:await u(s)},15e3);if("error"in t)throw new Error(t.error.message);return Number(t.data.timestamp)}async joinAwareness(e){const s=await this.emitWithAck("space:join-awareness",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,clientVersion:"1.0.0"},12e3);if("error"in s)throw new Error(s.error.message);if(!s.data.success)throw new Error("Failed to join awareness")}leaveAwareness(e){this.socket.emit("space:leave-awareness",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind})}onAwarenessCollect(e,s){const t=o=>{o?.spaceId===this.projectId&&String(o?.docId)===e&&s()};return this.socket.on("space:collect-awareness",t),()=>this.socket.off("space:collect-awareness",t)}onAwarenessUpdate(e,s){const t=o=>{o?.spaceId===this.projectId&&String(o?.docId)===e&&s(p(String(o.awarenessUpdate)))};return this.socket.on("space:broadcast-awareness-update",t),()=>this.socket.off("space:broadcast-awareness-update",t)}async broadcastAwareness(e,s){this.socket.emit("space:update-awareness",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind,awarenessUpdate:await u(s)})}requestAwarenesses(e){this.socket.emit("space:load-awarenesses",{spaceType:this.spaceType,spaceId:this.projectId,docId:e,docKind:this.docKind})}}export{j as P};

package/src/ui/dist/assets/{zoom-out-R-GWEhzS.js → zoom-out-DAukFWen.js}

@@ -1,11 +1,11 @@
-import{y as e}from"./index-Gbl53BNp.js";/**
+import{t as e}from"./index-CHzJ2xtB.js";/**
  * @license lucide-react v0.511.0 - ISC
  *
  * This source code is licensed under the ISC license.
  * See the LICENSE file in the root directory of this source tree.
- */const y=[["circle",{cx:"11",cy:"11",r:"8",key:"4ej97u"}],["line",{x1:"21",x2:"16.65",y1:"21",y2:"16.65",key:"13gj7c"}],["line",{x1:"11",x2:"11",y1:"8",y2:"14",key:"1vmskp"}],["line",{x1:"8",x2:"14",y1:"11",y2:"11",key:"durymu"}]],n=e("zoom-in",y);/**
+ */const o=[["circle",{cx:"11",cy:"11",r:"8",key:"4ej97u"}],["line",{x1:"21",x2:"16.65",y1:"21",y2:"16.65",key:"13gj7c"}],["line",{x1:"11",x2:"11",y1:"8",y2:"14",key:"1vmskp"}],["line",{x1:"8",x2:"14",y1:"11",y2:"11",key:"durymu"}]],n=e("zoom-in",o);/**
  * @license lucide-react v0.511.0 - ISC
  *
  * This source code is licensed under the ISC license.
  * See the LICENSE file in the root directory of this source tree.
- */const o=[["circle",{cx:"11",cy:"11",r:"8",key:"4ej97u"}],["line",{x1:"21",x2:"16.65",y1:"21",y2:"16.65",key:"13gj7c"}],["line",{x1:"8",x2:"14",y1:"11",y2:"11",key:"durymu"}]],x=e("zoom-out",o);export{x as Z,n as a};
+ */const y=[["circle",{cx:"11",cy:"11",r:"8",key:"4ej97u"}],["line",{x1:"21",x2:"16.65",y1:"21",y2:"16.65",key:"13gj7c"}],["line",{x1:"8",x2:"14",y1:"11",y2:"11",key:"durymu"}]],x=e("zoom-out",y);export{x as Z,n as a};

package/src/ui/dist/index.html

@@ -12,11 +12,11 @@
     <link rel="shortcut icon" href="/ui/logo-small.png" />
     <link rel="apple-touch-icon" href="/ui/logo-small.png" />
     <link rel="stylesheet" href="/ui/assets/fonts/ds-fonts.css" />
-    <script type="module" crossorigin src="/ui/assets/index-Gbl53BNp.js"></script>
+    <script type="module" crossorigin src="/ui/assets/index-CHzJ2xtB.js"></script>
     <link rel="modulepreload" crossorigin href="/ui/assets/plugin-terminal-MXFIPun8.js">
     <link rel="modulepreload" crossorigin href="/ui/assets/plugin-monaco-C8UgLomw.js">
-    <link rel="modulepreload" crossorigin href="/ui/assets/plugin-notebook-HbW2K-1c.js">
-    <link rel="stylesheet" crossorigin href="/ui/assets/index-Cgla8biy.css">
+    <link rel="modulepreload" crossorigin href="/ui/assets/plugin-notebook-JRhysCqj.js">
+    <link rel="stylesheet" crossorigin href="/ui/assets/index-DH-zxoZ3.css">
   </head>
   <body>
     <noscript>DeepScientist Copilot requires JavaScript.</noscript>

package/src/skills/analysis-campaign/references/artifact-orchestration.md

@@ -1,58 +0,0 @@
-# Artifact Orchestration For Analysis Campaigns
-
-Use this reference because the current runtime has no dedicated `campaign` artifact kind.
-
-## Recommended sequence
-
-1. **Launch decision**
-   - write `decision(action='launch_analysis_campaign')`
-   - include `campaign_id`, `parent_run_id` or `parent_idea_id`, and the reason
-2. **Campaign charter**
-   - write a `report` artifact for the planned slices
-3. **Isolation setup**
-   - call `artifact.prepare_branch(...)` only for slices that need code or config divergence
-   - reuse the current quest branch for pure reruns when possible
-4. **Execution updates**
-   - emit `progress` during long-running slices
-5. **Per-slice result**
-   - write one `run` artifact per slice
-6. **Campaign synthesis**
-   - write one aggregated `report`
-7. **Next-step routing**
-   - write one closing `decision`
-
-## Recommended per-slice fields
-
-Because `artifact.record(payload={...})` accepts extra fields, include:
-
-- `campaign_id`
-- `slice_id`
-- `run_kind`
-- `parent_run_id`
-- `analysis_question`
-- `fixed_conditions`
-- `changed_factors`
-- `success_criteria`
-- `abandonment_criteria`
-- `metrics_summary`
-- `metric_deltas`
-- `verdict`
-- `paths`
-
-## Naming guidance
-
-Suggested `run_kind` values:
-
-- `analysis.ablation`
-- `analysis.robustness`
-- `analysis.sensitivity`
-- `analysis.error`
-- `analysis.efficiency`
-- `analysis.environment`
-
-Suggested durable path layout:
-
-- `.ds/worktrees/<slice_id>/`
-- `experiments/analysis/<campaign_id>/<slice_id>/`
-- `artifacts/runs/<artifact_id>.json`
-- `artifacts/reports/<artifact_id>.json`

package/src/skills/baseline/references/memory-playbook.md

@@ -1,40 +0,0 @@
-# Baseline Memory Playbook
-
-Use this reference when deciding what should be stored in quest memory versus global memory during `baseline`.
-
-## Quest memory
-
-Use quest memory for:
-
-- baseline-specific setup failures
-- dataset or metric caveats tied to this quest
-- route-selection rationale
-- paper-to-code mismatch notes
-- accepted baseline caveats that later stages must remember
-
-## Global memory
-
-Promote to global only when the lesson is reusable, such as:
-
-- stable environment fixes
-- reproducibility heuristics
-- verification heuristics
-- broadly useful dataset or benchmark caveats
-
-## Kinds
-
-- `episodes`:
-  - failures
-  - repair attempts
-  - environment incidents
-- `knowledge`:
-  - stable lessons
-  - reproducibility rules
-  - accepted caveats
-- `decisions`:
-  - route and acceptance rationale
-
-## Promotion rule
-
-Do not promote a lesson to global just because it was painful.
-Promote it only if another quest is likely to benefit from it.

package/src/skills/baseline/references/publishable-baseline-package.md

@@ -1,30 +0,0 @@
-# Publishable Baseline Package
-
-Use this reference before attaching or publishing a baseline for reuse.
-
-## Minimum package contents
-
-- baseline identity
-- route used: attach, import, reproduce, or repair
-- source provenance
-- trusted metrics
-- exact path to the baseline root
-- command or execution summary
-- verification summary
-- key caveats
-
-## Strong package contents
-
-- variant structure
-- environment summary
-- config snapshot pointers
-- logs and result paths
-- explicit statement of downstream trust
-- explicit statement of global reusability
-
-## Do not publish if
-
-- verification is incomplete
-- metrics are not trusted
-- the result is only operational but incomparable
-- provenance is weak or undocumented

package/src/skills/write/references/outline-evidence-contract-example.md

@@ -1,107 +0,0 @@
-# Outline-Centered Paper Contract Example
-
-Use this reference when the paper line needs a concrete example of:
-
-- what a selected outline should look like before follow-up analysis
-- how completed evidence should be written back into the outline
-- what should block further drafting
-
-## Minimal selected outline shape
-
-```json
-{
-  "outline_id": "outline-002",
-  "title": "Truth-Preserving Collaboration under Mixed Signals",
-  "story": "Motivation -> bottleneck -> remedy -> evidence -> boundary",
-  "detailed_outline": {
-    "research_questions": [
-      "RQ1: Does the method improve the main benchmark under the accepted protocol?",
-      "RQ2: Which component actually causes the gain?",
-      "RQ3: Where does the method fail or regress?"
-    ],
-    "experimental_designs": [
-      "Main benchmark comparison",
-      "Component ablation",
-      "Boundary / failure analysis"
-    ],
-    "contributions": [
-      "A new route for source-aware collaboration",
-      "A controlled decomposition of the gain",
-      "A clearer limitation boundary"
-    ]
-  },
-  "evidence_contract": {
-    "main_text_items_must_be_ready": true,
-    "appendix_items_may_be_ready_or_reference_only": true,
-    "record_results_back_into_outline": true,
-    "result_table_required": true
-  },
-  "sections": [
-    {
-      "section_id": "results-main",
-      "title": "Main Results",
-      "paper_role": "main_text",
-      "claims": ["C1"],
-      "required_items": ["run-main-001"],
-      "optional_items": [],
-      "status": "pending",
-      "result_table": []
-    },
-    {
-      "section_id": "analysis-mechanism",
-      "title": "Mechanism Analysis",
-      "paper_role": "main_text",
-      "claims": ["C2"],
-      "required_items": ["AN-ABL-001"],
-      "optional_items": [],
-      "status": "pending",
-      "result_table": []
-    },
-    {
-      "section_id": "analysis-boundary",
-      "title": "Boundary and Failure Analysis",
-      "paper_role": "appendix",
-      "claims": ["C3"],
-      "required_items": [],
-      "optional_items": ["AN-BND-001"],
-      "status": "planned",
-      "result_table": []
-    }
-  ]
-}
-```
-
-## After one completed analysis slice
-
-Write the result back into the matching `section.result_table`.
-
-```json
-{
-  "item_id": "AN-ABL-001",
-  "title": "Remove corroboration module",
-  "kind": "analysis_slice",
-  "paper_role": "main_text",
-  "status": "completed",
-  "claim_links": ["C2"],
-  "metric_summary": "acc=0.811; delta=-0.046",
-  "result_summary": "Removing the corroboration module eliminates most of the measured gain.",
-  "source_paths": [
-    "experiments/analysis/analysis-1234/ablation/RESULT.md",
-    "experiments/analysis-results/analysis-1234/ablation.md"
-  ],
-  "updated_at": "2026-03-28T00:00:00Z"
-}
-```
-
-The matching section should then move from `pending` to:
-
-- `ready` if every required item is ready
-- `partial` if some required items are ready
-- `pending` if the row exists but the result is not ready
-
-## Drafting rules by case
-
-- If a section has missing required items, stop prose expansion and repair the evidence contract first.
-- If an analysis slice is completed but has no `section_id` or `item_id`, do not summarize it in the paper yet; map it first.
-- If a result is only useful as support, keep it in `appendix` or `reference_only` instead of inflating the main text.
-- If the result weakens the claim, record that downgrade in the outline before rewriting the section prose.

package/src/skills/write/references/paper-experiment-matrix-template.md

@@ -1,131 +0,0 @@
-# Paper Experiment Matrix Template
-
-Use this template when a paper-like line needs a durable experiment-control surface beyond the selected outline.
-
-Create and maintain both:
-
-- `paper/paper_experiment_matrix.md`
-- `paper/paper_experiment_matrix.json`
-
-The Markdown file is the human-facing control surface.
-The JSON file is the machine-facing mirror.
-
-## 1. Current Judgment
-
-- current judgment:
-- why the matrix is needed now:
-- what would make the experiments section stable:
-- what still blocks stable paper writing:
-
-## 2. Core Claims
-
-- `C1`:
-  - one-line claim:
-  - current support status:
-  - strongest current evidence:
-  - still-missing evidence:
-
-- `C2`:
-  - one-line claim:
-  - current support status:
-  - strongest current evidence:
-  - still-missing evidence:
-
-- `C3`:
-  - one-line claim:
-  - current support status:
-  - strongest current evidence:
-  - still-missing evidence:
-
-## 3. Highlight Hypotheses
-
-Write only serious hypotheses that could matter to the paper's reader-facing value.
-Do not assume the highlight is already true just because it sounds attractive.
-
-- `H1`:
-  - one-line highlight:
-  - why it is plausible:
-  - validation rows:
-  - fallback if unsupported:
-
-- `H2`:
-  - one-line highlight:
-  - why it is plausible:
-  - validation rows:
-  - fallback if unsupported:
-
-## 4. Taxonomy Summary
-
-Check every category deliberately.
-Do not collapse the matrix into “analysis only”.
-
-- main comparison:
-- component ablation:
-- sensitivity:
-- robustness:
-- efficiency / cost:
-- highlight validation:
-- failure boundary:
-- case study optional:
-
-## 5. Matrix Table
-
-| Exp id | Title | Tier | Experiment type | Status | Feasibility now | Claim ids | Highlight ids | Research question | Metrics | Paper placement | Next action |
-|---|---|---|---|---|---|---|---|---|---|---|---|
-| | | main_required / main_optional / appendix / optional / dropped | main_comparison / component_ablation / sensitivity / robustness / efficiency_cost / highlight_validation / failure_boundary / case_study_optional | proposed / planned / ready / running / completed / analyzed / written / excluded / blocked | feasible_now / light_setup / blocked / uncertain | | | | | main_text / appendix / maybe / omit | |
-
-## 6. Detail Cards
-
-Repeat one card per meaningful row.
-
-### EXP-001
-
-- title:
-- tier:
-- experiment type:
-- current status:
-- feasibility now:
-- why this row exists:
-- research question:
-- hypothesis:
-- comparators:
-- fixed conditions:
-- changed variables:
-- required metric(s):
-- minimal success criterion:
-- cost / runtime budget:
-- promotion rule:
-  - main text if:
-  - appendix if:
-  - omit if:
-- expected figure or table:
-- result artifact paths:
-- dependencies:
-- next action:
-
-## 7. Execution Frontier
-
-- rows ready now:
-- rows blocked now:
-- rows that must finish before the experiments section is stable:
-- rows that are appendix-only and can wait:
-- rows that are optional and should not block:
-
-## 8. Main-Text Gate
-
-Do not treat the experiments section as stable while any currently feasible row that is not merely `optional` or `dropped` remains unresolved.
-
-Every currently feasible non-optional row should be one of:
-
-- completed
-- analyzed
-- excluded with reason
-- blocked with reason
-
-## 9. Refresh Log
-
-After every completed, excluded, or blocked slice, reopen the matrix first and update it before selecting the next run.
-
-| Time | Exp id | What changed | Claim/highlight impact | Priority change | New next action |
-|---|---|---|---|---|---|
-| | | | | | |

package/src/skills/write/references/paper-section-playbook.md

@@ -1,64 +0,0 @@
-# Paper Section Playbook
-
-Use this reference when the output is a paper or paper-like report.
-
-## Introduction
-
-The introduction should usually answer:
-
-- why this problem matters now
-- what the baseline or prevailing route does
-- what concrete bottleneck remains
-- what the quest changed
-- what evidence supports that change
-- what the contribution scope really is
-
-After experiments stabilize, revisit the introduction and shrink any claim that no longer matches the evidence.
-
-## Related work
-
-Do more than list papers.
-Show:
-
-- which prior routes are closest
-- which assumption, mechanism, or scope differs
-- why the current quest is not just a rename of prior work
-
-## Method
-
-Keep the method section faithful to the implemented path:
-
-- no fictional components
-- no omitted caveats that materially change interpretation
-- no theory section detached from the code
-
-If equations are used:
-
-- define symbols
-- tie the objective or mechanism back to the implementation
-- avoid decorative math that explains nothing
-
-## Experiments
-
-Prefer this flow:
-
-1. setup and evaluation contract
-2. main comparison
-3. ablations or component analysis
-4. robustness or error analysis
-5. limitations visible from the results
-
-All numerical claims should point to specific tables, figures, or artifact paths.
-
-## Limitations
-
-Limitations should be concrete:
-
-- what was not tested
-- what remained unstable
-- which claims were intentionally downgraded
-- which comparisons were not comparable enough to use
-
-## Conclusion
-
-The conclusion should summarize what was actually shown, not restate the highest hope from the start of the quest.

package/src/skills/write/references/reviewer-first-writing.md

@@ -1,64 +0,0 @@
-# Reviewer-First Writing
-
-Use this reference when the draft needs to be organized around how reviewers and readers actually scan papers.
-
-## Core assumption
-
-Do not assume a reviewer will patiently reconstruct the paper for you.
-Assume the first judgment is formed quickly from:
-
-1. title
-2. abstract
-3. introduction opening
-4. first decisive figure or table
-5. final main-result section
-
-## Five-minute pass
-
-Before treating a draft as structurally sound, simulate a fast first pass and record:
-
-- what the paper claims in one sentence
-- what the main problem is
-- what the current-best route fails to do
-- what the method changes
-- what the strongest evidence is
-- whether the main claim still survives after that quick pass
-
-Suggested durable output:
-
-- `paper/reviewer_first_pass.md`
-
-## Reader-first organization
-
-Organize for reader understanding, not author chronology.
-
-Prefer this flow:
-
-- problem
-- challenge or bottleneck in the strongest prior route
-- intervention
-- evidence
-- boundary of the claim
-
-Avoid writing sections that merely replay the order in which the code or experiments were built.
-
-## First-page discipline
-
-When the deliverable is paper-like:
-
-- avoid wasting early page real estate on generic boilerplate
-- prefer direct contributions over “This paper is organized as follows”
-- if a figure or table is the fastest way to communicate the main result, place it early
-
-## Reader questions
-
-Every major section should answer a concrete reader question.
-
-Examples:
-
-- why does this problem matter now?
-- why are strong existing methods still insufficient?
-- what exactly changed?
-- why should that change help?
-- what evidence shows it helped?
-- where does the claim stop?

package/src/skills/write/references/revision-checklist.md

@@ -1,70 +0,0 @@
-# Revision Checklist
-
-Use this checklist when a draft is moving from “roughly complete” to “credible handoff”.
-
-## Review packet expectations
-
-A strong review packet should cover:
-
-- overall assessment
-- strongest aspects
-- weakest aspects
-- publication-readiness recommendation
-- section-by-section issues
-- concrete fixes
-- open author questions
-
-For each important issue, record:
-
-- location
-- severity: `critical`, `major`, or `minor`
-- description
-- suggested remediation
-- whether it blocks `finalize`
-
-## Five-pass revision default
-
-When the deliverable is a paper bundle, use this default unless there is a good reason not to:
-
-1. **Accuracy pass**
-   - remove unsupported claims
-   - repair method-description mismatch
-   - verify all important numbers against source artifacts
-2. **Structure pass**
-   - verify file inclusion / section organization
-   - ensure tables, figures, appendices, and references are reachable and named consistently
-   - confirm main-text vs appendix placement still makes sense
-3. **Narrative pass**
-   - repair logical jumps
-   - tighten transitions
-   - make sure motivation, challenge, resolution, validation, and impact still match the evidence
-4. **Presentation pass**
-   - polish wording
-   - fix citations
-   - fix table and figure captions
-   - fix proofing defects
-5. **Final verification pass**
-   - re-check the claim-evidence map
-   - re-check submission checklist items
-   - ensure no last-minute edits weakened accuracy
-
-## Validation categories
-
-Before declaring writing ready, verify at least these categories:
-
-- content authenticity and claim accuracy
-- structural completeness
-- experiment/result correspondence
-- citation integrity
-- formatting and readability
-- proofing and render quality
-- packaging completeness
-- handoff readiness
-
-## Failure handling
-
-If any `critical` issue remains:
-
-- do not mark the bundle ready
-- record the exact blocker
-- either continue the revision loop or route back through `decision`