superlab 0.1.13 → 0.1.15

package/package-assets/shared/skills/lab/references/paper-writing/examples/method/module-triad-neural-body.md

@@ -0,0 +1,19 @@
+# Module Triad Example (Neural Body)
+
+`Use Neural Body to understand the three elements of a module: design, motivation, and technical advantages.`
+
+Local source references:
+
+1. Annotated figure showing motivation/design/advantages split.
+3. Text-converted annotation notes: `references/examples/method/neural-body-annotated-figure-text.md`
+
+Triad mapping template:
+
+1. Module design: what representation/network is built and how forward process runs.
+2. Motivation: what unresolved challenge requires this module.
+3. Technical advantages: why this module performs better than alternatives.
+
+Direct usage:
+
+1. Read `neural-body-annotated-figure-text.md` to map each paragraph to one triad element.
+2. Rebuild your own Method subsection with the same triad order.

package/package-assets/shared/skills/lab/references/paper-writing/examples/method/neural-body-annotated-figure-text.md

@@ -0,0 +1,66 @@
+# Neural Body Annotated Figure (Text Conversion)
+
+This file converts the annotated Neural Body figure into reusable writing notes.
+
+## Purpose
+
+Use this mapping to understand how one Method section can explicitly separate:
+
+1. Module motivation
+2. Module design (data structure)
+3. Module design (forward process)
+4. Technical advantages
+
+## Block-by-Block Mapping
+
+### Section 3.1: Structured Latent Codes
+
+1. **Module design (data structure)**
+- The paragraph defines structured latent codes anchored to the deformable human model (SMPL).
+- It explains what is constructed (latent codes + their anchor positions + frame-dependent transformation by pose).
+
+2. **Technical advantages**
+- The paragraph explains why this design works better: dynamic-human representation and cross-frame integration of observations.
+- It highlights why anchoring codes to deformable geometry is beneficial.
+
+### Section 3.2: Code Diffusion
+
+1. **Motivation of this module**
+- The paragraph states the remaining problem: direct interpolation of sparse structured codes leads to near-zero vectors at many 3D points.
+- This motivates diffusion from surface codes to nearby 3D space.
+
+2. **Module design (forward process)**
+- The paragraph explains the execution pipeline: build sparse latent volumes, run sparse convolutions, interpolate latent codes at query points, and feed codes to prediction networks.
+- This is a canonical input -> steps -> output module description.
+
+### Section 3.3: Density and Color Regression
+
+1. **Module design (forward process) for density model**
+- The density paragraph defines how density is regressed from latent code and frame condition.
+
+2. **Module design (data structure) for color model**
+- The color paragraph introduces required inputs/embeddings (latent code, view direction, spatial location, temporal embedding).
+
+3. **Module design (forward process) for color model**
+- The next paragraph describes how those inputs are encoded and passed into the color MLP for final color prediction.
+
+### Section 3.4: Volume Rendering
+
+1. **Module design (forward process)**
+- The paragraph describes ray sampling and volume integration to render image outputs from predicted density/color fields.
+
+## Reusable Writing Pattern from This Figure
+
+For each module subsection, follow this order:
+
+1. `Motivation`: state unresolved challenge and technical reason.
+2. `Design-1`: define structure/representation/network.
+3. `Design-2`: describe forward process in execution order.
+4. `Advantage`: explain why this module improves over alternatives.
+
+## Suggested Paragraph Starters
+
+1. Motivation: `A remaining challenge is ...`
+2. Data structure design: `We represent ... with ...`
+3. Forward process: `Given [input], we first ... then ... finally ...`
+4. Technical advantage: `Compared with previous methods, this design ... because ...`

package/package-assets/shared/skills/lab/references/paper-writing/examples/method/overview-template.md

@@ -0,0 +1,30 @@
+# Method Overview Template
+
+
+`Overview usually includes setting, core contribution, optional figure pointer, and subsection map.`
+
+```latex
+% Overview
+% One or two sentences for setting
+%% Example 1: Given a sparse multi-view video of a performer, our task is to generate a free-viewpoint video of the performer.
+%% Example 2: Given an image, the task of pose estimation is to detect objects and estimate their orientations and translations in the 3D space.
+
+% One or two sentences for core contribution
+%% Example 1: We build upon prior work for static scenes [46], to which we add the notion of time, and estimate 3D motion by explicitly modeling forward and backward scene flow as dense 3D vector fields.
+%% Example 2: Inspired by [21, 25], we perform object segmentation by deforming an initial contour to match object boundary.
+%% Example 3: Inspired by recent methods [29, 30, 36], we estimate the object pose using a two-stage pipeline: we first detect 2D object keypoints using CNNs and then compute 6D pose parameters using the PnP algorithm. Our innovation is in a new representation for 2D object keypoints as well as a modified PnP algorithm for pose estimation.
+
+% If pipeline/framework is novel, point to figure
+%% Example: The overview of the proposed model is illustrated in Figure 3.
+
+% Explain what Section 3.1 covers
+%% Example 1: Neural Body starts from a set of structured latent codes attached to the surface of a deformable human model (Section 3.1).
+%% Example 2: In this section, we first describe how to model 3D scenes with MLP maps (Section 3.1).
+
+% Explain what Section 3.2 covers
+%% Example 1: The latent code at any location around the surface can be obtained with a code diffusion process (Section 3.2) and then decoded to density and color values by neural networks (Section 3.3).
+%% Example 2: Then, Section 3.2 discusses how to represent volumetric videos with dynamic MLP maps.
+
+% Explain what Section 3.3 covers
+%% Example 3: Finally, we introduce some strategies to speed up the rendering process (Section 3.3).
+```

package/package-assets/shared/skills/lab/references/paper-writing/examples/method/pre-writing-questions.md

@@ -0,0 +1,17 @@
+# Method Pre-Writing Questions
+
+
+`Before writing Method, answer: (1) what modules exist, and (2) for each module, what is its workflow, why is it needed, and why does it work.`
+
+```text
+Questions:
+(1) What modules are in the method?
+(2) For each module, answer three questions:
+    - What is this module's workflow?
+    - Why do we need this module?
+    - Why does this module work?
+```
+
+Recommended action:
+
+1. Organize answers in a mind map or table before writing paragraphs.

package/package-assets/shared/skills/lab/references/paper-writing/examples/method/section-skeleton.md

@@ -0,0 +1,9 @@
+# Method Section Skeleton
+
+```latex
+\section{Method}
+% Overview
+% Section 3.1
+% Section 3.2
+% Section 3.3
+```

package/package-assets/shared/skills/lab/references/paper-writing/examples/method-examples.md

@@ -0,0 +1,24 @@
+# Method Examples Index
+
+All method example cites should point to the local files below.
+
+## A. Planning and Writing Workflow
+
+1. Pre-writing questions: `references/examples/method/pre-writing-questions.md`
+
+## B. Module Triad and Module-Level Writing
+
+1. Module triad (Neural Body): `references/examples/method/module-triad-neural-body.md`
+2. Neural Body figure text conversion: `references/examples/method/neural-body-annotated-figure-text.md`
+3. Module design (Instant-NGP): `references/examples/method/module-design-instant-ngp.md`
+4. Module motivation patterns: `references/examples/method/module-motivation-patterns.md`
+
+## C. Section-Level Templates
+
+1. Method section skeleton: `references/examples/method/section-skeleton.md`
+2. Overview template: `references/examples/method/overview-template.md`
+3. Example of the three elements: `references/examples/method/example-of-the-three-elements.md`
+
+## D. Clarity and Troubleshooting
+
+1. Common issues note: `references/examples/method/method-writing-common-issues-note.md`

package/package-assets/shared/skills/lab/references/paper-writing/introduction.md

@@ -337,7 +337,13 @@ Why not recommended (writing structure warning):
 
 ## Usage Note
 
-This vendored guide keeps the introduction patterns but omits the original example-bank files. Treat the templates and sentence skeletons here as the canonical reference inside `superlab`.
+This vendored guide should be paired with the local introduction example bank:
+
+- `references/examples/index.md`
+- `references/examples/introduction-examples.md`
+- 1-2 matching files under `references/examples/introduction/`
+
+Use the introduction patterns and sentence skeletons here first, then use the example files to choose a concrete paragraph flow and narrative progression. Reuse structure, not wording.
 
 ## Quick Quality Checklist
 

package/package-assets/shared/skills/lab/references/paper-writing/method.md

@@ -62,7 +62,11 @@ Definition:
 
 ### Example of the Three Elements
 
-Use the structure above directly. The original example-bank files are not bundled in `superlab`.
+Use the structure above directly, then compare it with the local method example bank:
+
+- `references/examples/index.md`
+- `references/examples/method-examples.md`
+- 1-2 matching files under `references/examples/method/`
 
 ## Method Content Decomposition
 
@@ -163,4 +167,4 @@ flowchart TB
 
 ## Usage Note
 
-This vendored guide keeps the method-writing patterns and checklists but does not bundle the upstream example-bank files. Treat the subsection structures, sentence skeletons, and review questions in this file as the direct working reference.
+This vendored guide should be paired with the local method example bank listed above. Use this file for subsection structure, module-writing checks, and review questions first; then use the example files to choose a concrete presentation pattern. Reuse structure, not wording.

package/package-assets/shared/skills/lab/references/paper-writing-integration.md

@@ -2,11 +2,13 @@
 
 `/lab:write` vendors the paper-writing references directly into `skills/lab/references/paper-writing/`.
 The goal is to keep the upstream writing discipline while removing brittle runtime dependence on a separately installed skill.
+It also vendors the upstream example bank for the sections that currently have curated examples, so drafting can reuse concrete structure rather than only abstract guidance.
 
 ## Role Split
 
 - `lab` controls stage boundaries, evidence discipline, and durable artifacts.
 - the vendored paper-writing references control section structure, paragraph logic, and reviewer-facing polish.
+- the vendored example bank controls example-driven structure selection for `abstract`, `introduction`, and `method`.
 - `/lab:write` links evidence-backed research outputs to paper-ready text.
 
 ## Required Shared Constraints
@@ -33,6 +35,30 @@ The goal is to keep the upstream writing discipline while removing brittle runti
 - `paper-writing/paper-review.md`
 - `paper-writing/does-my-writing-flow-source.md`
 
+## Vendored Example Bank
+
+- `paper-writing/examples/index.md`
+- `paper-writing/examples/abstract-examples.md`
+- `paper-writing/examples/introduction-examples.md`
+- `paper-writing/examples/method-examples.md`
+- `paper-writing/examples/abstract/*`
+- `paper-writing/examples/introduction/*`
+- `paper-writing/examples/method/*`
+
+## Write-Time Rule
+
+For `abstract`, `introduction`, and `method`:
+
+1. read the section guide first
+2. read the matching examples index
+3. read 1-2 concrete example files that match the intended structure
+4. reuse structure and sentence logic without copying wording
+
+For `related work`, `experiments`, and `conclusion`:
+
+1. use the section guide directly
+2. do not invent non-existent example-bank files
+
 ## Attribution
 
 These references are adapted from:

package/package-assets/shared/skills/lab/stages/auto.md

@@ -38,6 +38,7 @@
 - Treat `/lab:auto` as an orchestration layer, not a replacement for existing `/lab:*` stages.
 - Treat `.lab/context/eval-protocol.md` as the source of truth for paper-facing metrics, metric glossary, table plan, gates, and structured experiment ladders.
 - Treat the evaluation protocol as source-backed, not imagination-backed: metric definitions, baseline behavior, comparison implementations, and deviations must come from recorded sources before they are used in gates or promotions.
+- Treat paper-template selection as an explicit write-time gate, not as a silent fallback, when the loop is about to create `.tex` deliverables for the first time.
 - The contract must declare `Autonomy level` and `Approval status`, and execution starts only when approval is explicitly set to `approved`.
 - The contract must also declare a concrete terminal goal:
   - `rounds`
@@ -54,6 +55,8 @@
 - You may promote exploratory additions to the primary package only when the contract's promotion policy is satisfied and the promotion is written back into `data-decisions.md`, `decisions.md`, `state.md`, and `session-brief.md`.
 - Poll long-running commands until they finish, hit a timeout, or hit a stop condition.
 - Keep a poll-based waiting loop instead of sleeping blindly.
+- Do not treat a short watcher such as `sleep 30`, a one-shot `pgrep`, or a single `metrics.json` probe as the rung command when the real experiment is still running.
+- Bind each rung to the real long-running command or process that owns the experiment result.
 - Always write a canonical `.lab/context/auto-outcome.md` when the run completes, stops, or fails.
 - When the evaluation protocol declares structured ladder rungs, execute them as a foreground rung state machine:
   - each rung must declare `Stage`, `Goal`, `Command`, `Watch`, `Gate`, `On pass`, `On fail`, and `On stop`
@@ -63,7 +66,7 @@
 - Enforce stage contracts, not just exit codes:
   - `run` and `iterate` must change persistent outputs under `results_root`
   - `review` must update canonical review context
-  - `report` must produce `<deliverables_root>/report.md`
+  - `report` must produce `<deliverables_root>/report.md` and `<deliverables_root>/main-tables.md`
   - `write` must produce LaTeX output under `<deliverables_root>/paper/`
 - Treat promotion as incomplete unless it writes back to `data-decisions.md`, `decisions.md`, `state.md`, and `session-brief.md`.
 - Do not stop or promote on the basis of a metric or comparison claim whose source-backed definition is missing from the approved evaluation protocol.
@@ -87,3 +90,28 @@
 - If the contract is incomplete, ask one clarifying question at a time.
 - If multiple next actions are credible, present 2-3 bounded options with trade-offs before arming a long run.
 - Only ask for approval when the next step would leave the approved exploration envelope, exceed the chosen autonomy level, or materially change the frozen core.
+
+## Input Normalization
+
+- Normalize ambiguous user requests before arming the loop.
+- Treat `Autonomy level L1/L2/L3` as execution privilege only.
+- Treat `Layer`, `Phase`, and `Table` references as paper-structure or experiment-scope targets, not as autonomy levels.
+- Example:
+  - `Layer 3 organizer enforcement` means a paper layer or experiment target.
+  - `Autonomy level L3` means the aggressive campaign permission envelope.
+- If the user mixes framework work and experiment work in one request, restate a normalized contract with:
+  - objective
+  - autonomy level
+  - terminal goal
+  - scope
+  - allowed modifications
+- Then ask at most one clarifying question if a blocking field is still missing.
+- If `.lab/config/workflow.json` sets the workflow language to Chinese, write summaries, options, checklist items, task labels, and progress updates in Chinese unless a file path, code identifier, or literal metric name must remain unchanged.
+- When the loop reaches `report`, apply the same workflow-language rule to `report.md` and the managed `main-tables.md` artifact.
+- When the loop is about to enter `write` and `paper_template_root` is empty:
+  - if `paper_template_decision` is `unconfirmed`, ask one explicit question: continue with the default scaffold or attach a template directory first
+  - if the user chooses the default scaffold, persist `paper_template_decision: default-scaffold`
+  - if the user chooses a template, stop the loop and route to `superlab paper attach-template --path <dir>`
+  - if the current write target is a final manuscript export, `paper_template_decision` is `default-scaffold`, and `paper_template_final_reminder_acknowledged` is `false`, ask one final reminder question before finalizing
+  - if the user confirms staying on the default scaffold at that final reminder, persist `paper_template_final_reminder_acknowledged: true`
+- While the real experiment process is still alive, emit only a progress update and keep waiting. Do not present a terminal summary for that rung until the process exits or the rung hits an explicit stop boundary.

package/package-assets/shared/skills/lab/stages/report.md

@@ -3,8 +3,10 @@
 ## Required Output
 
 - method overview
+- selected metrics summary
 - experiment setup
 - validated main results
+- managed main tables artifact under `<deliverables_root>/main-tables.md`
 - ablations
 - failed attempts
 - limitations
@@ -31,13 +33,15 @@
 - Tie every major claim to recorded summaries or iteration artifacts.
 - Structure tables, gates, and main claims against the approved evaluation protocol.
 - Do not restate metric definitions, baseline behavior, or comparison implementations from memory; use the approved evaluation protocol and its recorded sources.
+- Carry the approved `Primary metrics`, `Secondary metrics`, and `Required terminal evidence` into both the report and the managed main-tables artifact.
 - If the report depends on a deviation from an original metric or implementation, state that deviation explicitly instead of smoothing it over.
+- If `.lab/config/workflow.json` sets the workflow language to Chinese, write `report.md` and `<deliverables_root>/main-tables.md` in Chinese unless a file path, code identifier, or literal metric name must remain unchanged.
 - Prefer conservative interpretation over marketing language.
 - Leave a clear handoff path into `/lab:write` with evidence links that section drafts can cite.
 
 ## Interaction Contract
 
-- Start with a concise summary of the campaign outcome, strongest supported claim, and biggest reporting risk.
+- Start with a concise summary of the campaign outcome, the selected primary and secondary metrics, the strongest supported claim, and the biggest reporting risk.
 - If a missing assumption would change report interpretation, ask one clarifying question at a time.
 - If there are multiple defensible report framings, present 2-3 approaches with trade-offs and recommend the most evidence-faithful framing before writing.
 - Keep an approval gate when the reporting frame would materially affect what the paper later claims.

package/package-assets/shared/skills/lab/stages/write.md

@@ -13,6 +13,8 @@
 
 - `.lab/config/workflow.json`
 - `paper_template_root` from `.lab/config/workflow.json`
+- `paper_template_decision` from `.lab/config/workflow.json`
+- `paper_template_final_reminder_acknowledged` from `.lab/config/workflow.json`
 
 ## Context Read Set
 
@@ -38,6 +40,12 @@ Load the exact vendored file that matches the current target:
 - experiments -> `skills/lab/references/paper-writing/experiments.md`
 - conclusion -> `skills/lab/references/paper-writing/conclusion.md`
 
+When the current target has a bundled example bank, load the examples index and 1-2 concrete example files that match the intended structure:
+
+- abstract -> `skills/lab/references/paper-writing/examples/index.md`, `skills/lab/references/paper-writing/examples/abstract-examples.md`, plus one matching file under `skills/lab/references/paper-writing/examples/abstract/`
+- introduction -> `skills/lab/references/paper-writing/examples/index.md`, `skills/lab/references/paper-writing/examples/introduction-examples.md`, plus 1-2 matching files under `skills/lab/references/paper-writing/examples/introduction/`
+- method -> `skills/lab/references/paper-writing/examples/index.md`, `skills/lab/references/paper-writing/examples/method-examples.md`, plus 1-2 matching files under `skills/lab/references/paper-writing/examples/method/`
+
 Run these on every round:
 
 - section flow check -> `skills/lab/references/paper-writing/does-my-writing-flow-source.md`
@@ -49,8 +57,15 @@ Run these on every round:
 - LaTeX is the required manuscript output format.
 - If `paper_template_root` is configured, inspect that template directory before drafting and align the manuscript structure to it.
 - Treat attached template directories as user-owned and potentially modified. Do not rewrite template files unless the user explicitly asks.
-- If no paper template is configured, use the default LaTeX scaffold under the deliverable paper directory.
+- If no paper template is configured and `paper_template_decision` is `unconfirmed`, ask one explicit question before the first `.tex` drafting round: continue with the default LaTeX scaffold, or attach a template directory first.
+- If the user chooses the default scaffold, persist that choice in `.lab/config/workflow.json` by setting `paper_template_decision` to `default-scaffold`.
+- If the user chooses to attach a template, stop the drafting loop and route to `superlab paper attach-template --path <dir>` instead of silently falling back.
+- If `paper_template_decision` is `default-scaffold`, use the managed default LaTeX scaffold under the deliverable paper directory.
+- If the current round is a final manuscript export or final-draft pass, `paper_template_root` is still empty, `paper_template_decision` is `default-scaffold`, and `paper_template_final_reminder_acknowledged` is `false`, ask one final reminder question about switching to a template before finalizing.
+- If the user confirms staying on the default scaffold at that final reminder, persist `paper_template_final_reminder_acknowledged: true`.
 - Load only the current section guide. Do not load every section guide at once.
+- Reuse example-bank structure, paragraph roles, and sentence logic when examples are bundled, but never copy wording verbatim.
+- Treat example cites and example file names as writing references, not as evidence for the current paper.
 - Build a compact mini-outline before prose.
 - For each subsection, explicitly include motivation, design, and technical advantage when applicable.
 - Avoid a writing style that reads like incremental patching of a naive baseline.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "superlab",
-  "version": "0.1.13",
+  "version": "0.1.15",
   "description": "Strict /lab research workflow installer for Codex and Claude",
   "keywords": [
     "codex",