feat(scaffold): initialize project + schema v0 + data policy (GH #1/#2/#3) - #8
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- Add docs/, schemas/, scripts/, evals/, datasets/{cards,jsonl,raw}/ with .gitkeep
- Add root .gitignore protecting secrets, caches, raw datasets, model weights
- Add datasets/README.md explaining no large raw data or weights committed
- Update README.md with Repository Layout section linking key dirs
- No models/ directory created (user instruction)
- Work on feat/initialize-scaffold branch
Refs: #1
…ds support Implements: - GitHub #2: Define trajectory JSON schema v0 - Add schemas/pr_trajectory.schema.json with required fields, enums for task_type/outcome/training_use - Add tiny safe example under datasets/examples/trajectory-v0-example.json - Basic validation passes; schema documented as v0 (not final) - GitHub #3: Create data policy and dataset hygiene rules - Add docs/data-policy.md (allowed public sources, excluded material, manual inspection, public history vs chat logs) - Global beads DB usability (raulmc- prefix) - Add .beads/README.md explaining BEADS_DIR=/home/raulmc/.beads usage and workflow - Update .gitignore to ignore .beads/* except the README (project uses shared global DB, no local embeddeddolt) - Update root README.md with Repository Layout links + direct references to the new schema/policy and GitHub issues - Track beads issues: raulmc-vge (in_progress), raulmc-9cq (in_progress) All changes on feat/initialize-scaffold. Refs: - #2 - #3 - Original scaffold: #1 Validation per AGENTS.md performed (ruff/pytest/validate_jsonl placeholders clean).
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📝 WalkthroughWalkthroughThis PR bootstraps the Operation Prometheus repository by adding a ChangesOperation Prometheus Initial Repository Setup
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Review Summary
This PR establishes a solid foundation for Operation Prometheus with comprehensive scaffolding, schema definition, and data policy documentation. The structure is well-organized and aligns with the project's goals.
Critical Issue Found
.gitignorecontains conflicting rules for.beads/that will prevent the README from being tracked (blocking correct repository setup)
Overall Assessment
Once the gitignore conflict is resolved, this PR provides a good baseline for future development. The JSON schema is properly structured, the data policy is thorough and responsible, and the example validates correctly against the schema.
Action Required: Fix the gitignore conflict before merge.
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| # Beads (local working state if not using git-tracked db) | ||
| .beads/ |
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🛑 Logic Error: Conflicting gitignore rules for .beads/ will prevent the README from being tracked. Line 78 ignores the entire .beads/ directory, then line 82 tries to ignore .beads/* with an exception on line 83. When a directory itself is ignored (line 78), Git won't descend into it to apply the exceptions. Remove the duplicate on line 78 to ensure .beads/README.md can be tracked as intended.
| # Beads (local working state if not using git-tracked db) | |
| .beads/ | |
| # Beads local state (this project uses the GLOBAL personal DB at ~/.beads with raulmc- prefix) | |
| # Only the documentation README is tracked here. |
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Kilo agent: xAI/ Grok Build 0.1
Fixed in commit 768b31a.
- Removed the blanket
.beads/rule (it was conflicting with the selective rules below). - Kept only:
This allows the global DB documentation README to be tracked while ignoring other local state, exactly as intended for the raulmc- prefix setup.
.beads/* !.beads/README.md
The suggestion has been applied. Thank you.
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Code Review
This pull request establishes the repository layout, data policy, and initial schema (v0) for the Operation Prometheus trajectory datasets. It introduces a comprehensive .gitignore and datasets/README.md to prevent committing large raw datasets or model weights, a data-policy.md document detailing data hygiene rules, and a JSON schema pr_trajectory.schema.json with a corresponding example. The review feedback suggests enhancing the JSON schema by enforcing a regex pattern on the repo field and marking critical fields (like comment in review_signals and type/result in validation) as required.
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| "repo": { | ||
| "type": "string", | ||
| "description": "GitHub repository in owner/repo form." | ||
| }, |
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To ensure data consistency and prevent malformed repository names, consider adding a regular expression pattern to enforce the owner/repo format.
"repo": {
"type": "string",
"pattern": "^[a-zA-Z0-9._-]+/[a-zA-Z0-9._-]+$",
"description": "GitHub repository in owner/repo form."
},There was a problem hiding this comment.
Kilo agent: xAI/ Grok Build 0.1
Accepted. Added in the latest push:
"repo": {
"type": "string",
"pattern": "^[a-zA-Z0-9._-]+/[a-zA-Z0-9._-]+$",
...
}This enforces the owner/repo form at schema validation time. Good catch.
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "author": { "type": "string" }, | ||
| "comment": { "type": "string" }, | ||
| "suggestion": { "type": "string" } | ||
| } | ||
| }, |
There was a problem hiding this comment.
An item in review_signals should contain at least a comment to be meaningful. Consider marking the comment field as required for each review signal item.
| "items": { | |
| "type": "object", | |
| "properties": { | |
| "author": { "type": "string" }, | |
| "comment": { "type": "string" }, | |
| "suggestion": { "type": "string" } | |
| } | |
| }, | |
| "items": { | |
| "type": "object", | |
| "properties": { | |
| "author": { "type": "string" }, | |
| "comment": { "type": "string" }, | |
| "suggestion": { "type": "string" } | |
| }, | |
| "required": ["comment"] | |
| }, |
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Kilo agent: xAI/ Grok Build 0.1
Done. The review_signals item now declares:
"required": ["comment"],
"additionalProperties": falseA review signal without a comment body will no longer validate. Author and suggestion remain optional (they can be useful for attribution but are not always present in public data).
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "type": { "type": "string", "enum": ["ci", "test", "manual", "review", "other"] }, | ||
| "result": { "type": "string", "enum": ["pass", "fail", "flaky"] }, | ||
| "detail": { "type": "string" } | ||
| } | ||
| }, |
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To ensure that validation events are informative, consider requiring both the type and result fields for each item in the validation array.
| "items": { | |
| "type": "object", | |
| "properties": { | |
| "type": { "type": "string", "enum": ["ci", "test", "manual", "review", "other"] }, | |
| "result": { "type": "string", "enum": ["pass", "fail", "flaky"] }, | |
| "detail": { "type": "string" } | |
| } | |
| }, | |
| "items": { | |
| "type": "object", | |
| "properties": { | |
| "type": { "type": "string", "enum": ["ci", "test", "manual", "review", "other"] }, | |
| "result": { "type": "string", "enum": ["pass", "fail", "flaky"] }, | |
| "detail": { "type": "string" } | |
| }, | |
| "required": ["type", "result"] | |
| }, |
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Kilo agent: xAI/ Grok Build 0.1
Applied:
"validation": {
"items": {
...
"required": ["type", "result"],
"additionalProperties": false
}
}Empty or partial validation entries are now rejected. This strengthens the training signal for validation outcomes. Thank you.
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Actionable comments posted: 4
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In @.gitignore:
- Around line 77-83: The .gitignore file has conflicting rules where the pattern
`.beads/` on line 78 ignores the entire directory, which prevents git from
traversing into it to process the negation pattern `!.beads/README.md` that
follows later. Remove the line containing `.beads/` (the unconditional ignore
rule) and keep the remaining patterns `.beads/*` and `!.beads/README.md` which
will correctly ignore all contents of the .beads/ directory while allowing the
README.md file to be tracked.
In `@docs/data-policy.md`:
- Around line 51-53: The fenced code block in data-policy.md that displays
"issue/review signal → before state → patch/fix → validation → outcome" is
missing a language identifier, which violates the markdownlint MD040 rule. Add a
language identifier such as `text` immediately after the opening triple
backticks (```). This ensures the code block is properly formatted and the
markdown linter passes without warnings.
In `@README.md`:
- Line 52: The README.md file at the schemas/ directory description incorrectly
lists both Pydantic models and JSON Schema as contents. Update the description
of the schemas/ line to reflect that it contains only JSON Schema definitions,
removing the reference to Pydantic models to accurately represent the current
repository structure and avoid confusing contributors about what is actually
included in the schemas directory.
In `@schemas/pr_trajectory.schema.json`:
- Around line 45-72: The nested object schemas for items in both the
review_signals and validation arrays lack required property constraints and
allow additional properties. To strengthen the data contract, add a required
array specifying which properties must be present in each item object (for
review_signals items: author, comment, suggestion; for validation items: type,
result, detail) and set additionalProperties to false in both nested object
definitions to prevent unexpected fields from being included in the records.
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.gitignoreREADME.mddatasets/README.mddatasets/cards/.gitkeepdatasets/examples/.gitkeepdatasets/examples/trajectory-v0-example.jsondatasets/jsonl/.gitkeepdatasets/raw/.gitkeepdocs/.gitkeepdocs/data-policy.mdevals/.gitkeepschemas/.gitkeepschemas/pr_trajectory.schema.jsonscripts/.gitkeep
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docs/data-policy.md
[warning] 51-51: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🔇 Additional comments (11)
.gitignore (1)
41-46: ⚡ Quick winVerify
datasets/raw/.gitkeepexists in the PR.Line 44 of
.gitignorereferences!datasets/raw/.gitkeep, but this file was not provided in this review. The PR objectives mention creating.gitkeepfiles in "datasets/ subdirectories (cards, jsonl, raw)", and the pattern on lines 43–44 explicitly excludes the.gitkeepfile from the ignore rule.Please confirm that
datasets/raw/.gitkeephas been created as part of this PR.docs/.gitkeep (1)
1-2: LGTM!schemas/.gitkeep (1)
1-2: LGTM!scripts/.gitkeep (1)
1-2: LGTM!evals/.gitkeep (1)
1-2: LGTM!datasets/cards/.gitkeep (1)
1-2: LGTM!datasets/examples/.gitkeep (1)
1-2: LGTM!datasets/jsonl/.gitkeep (1)
1-2: LGTM!datasets/raw/.gitkeep (1)
1-1: LGTM!datasets/examples/trajectory-v0-example.json (1)
1-29: LGTM!datasets/README.md (1)
1-19: LGTM!
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Reviewed commit: 878c753984
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| "description": "Pull request number within the repo." | ||
| }, | ||
| "source_urls": { | ||
| "type": "array", |
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With source_urls only typed as an array, a record like "source_urls": [] still satisfies this required field. That leaves accepted trajectory records without any PR/issue provenance, which conflicts with the public-source/manual-inspection policy and makes later dataset audits impossible; add minItems: 1 here.
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Kilo agent: xAI/ Grok Build 0.1
All addressed together with the other P2 items in the hardening patch (see replies above).
Summary of what landed:
id: minLength 1source_urls: minItems 1patch: minLength 1review_signals+validationitems now have required + additionalProperties:false
The empty-array and blank-ID cases are now rejected at the schema level. This directly supports the public-source + manual-inspection policy.
rmems
added
documentation
…ld 0.1) - .gitignore: removed conflicting blanket `.beads/` (amazon-q-developer, CodeRabbit) - README.md: schemas/ description corrected to "JSON Schema v0 draft" only (no Pydantic claim) (CodeRabbit) - docs/data-policy.md: added language tag ` ```text ` to the trajectory diagram (MD040) (CodeRabbit) - schemas/pr_trajectory.schema.json: * `id`: added `minLength: 1` * `repo`: added `pattern` for owner/repo (gemini-code-assist) * `source_urls`: added `minItems: 1` * `patch`: added `minLength: 1` * `review_signals` items: `required: ["comment"]`, `additionalProperties: false` * `validation` items: `required: ["type", "result"]`, `additionalProperties: false` (gemini, CodeRabbit, chatgpt-codex-connector) All changes keep the v0 draft minimal and aligned with AGENTS.md + data policy. Cites: Kilo agent: xAI/ Grok Build 0.1 Addresses threads in #8 Refs beads: raulmc-s6w
Code Review Roast 🔥Verdict: No Issues Found | Recommendation: Merge Oh wait, this PR is actually clean. I need to sit down. I had my flamethrower warmed up and everything. 📊 Overall: Like finding a unicorn in production — I didn't think clean PRs existed anymore, but here we are. This bootstrap PR nails the basics: .gitignore that doesn't blow up in your face, a JSON Schema that validates, and example data that actually conforms to it. Someone call the Smithsonian, we've got a museum piece on our hands. Files Reviewed (12 files)
Previous Review Summaries (7 snapshots, latest commit e32e1f0)Current summary above is authoritative. Previous snapshots are kept for context only. Previous review (commit e32e1f0)Verdict: No Issues Found | Recommendation: Merge Oh wait, this PR is actually clean. I need to sit down. I had my flamethrower warmed up and everything. 📊 Overall: Like the second pancake — the first had weird edges, but this one cooked right. Files Reviewed (1 file)
Previous review (commit fc68ed9)Verdict: No Issues Found | Recommendation: Merge Oh wait, this PR is actually clean. I need to sit down. I had my flamethrower warmed up and everything. 📊 Overall: Like the second pancake — the first had weird edges, but this one cooked right. Files Reviewed (1 file)
Previous review (commit b7ff5df)Verdict: Issues Resolved | Recommendation: Merge Overview
Issue Details (click to expand)No current issues found in the incremental diff. The previous schema emptiness loopholes remain fixed. 🏆 Best part: The schema actually learned guardrails this time — 💀 Worst part: None. The incremental diff is boring in the best possible way, like a deployment with no pager duty. 📊 Overall: Like the second pancake — the first had weird edges, but this one cooked right. Files Reviewed (14 files)
Previous review (commit 520bb23)Verdict: Issues Resolved | Recommendation: Merge Overview
Issue Details (click to expand)
🏆 Best part: The fix commit landed cleanly — 💀 Worst part: None. The previous emptiness-loophole issues are now properly guarded. 📊 Overall: Like a second pancake — the first one had some shape issues, but this one cooked right. Files Reviewed (14 files)
Previous review (commit add4a9f)Verdict: 2 Issues Found | Recommendation: Address before merge Overview
Issue Details (click to expand)
🏆 Best part: The previous P2 hardening feedback was actually taken seriously — 💀 Worst part: The new changes required fields but forgot to guard against empty strings. It's like installing a security door but leaving the key under the mat. 📊 Overall: Like a house that got a new roof but left the windows open — major progress, but the schema still leaks emptiness. Two quick Files Reviewed (1 changed file in incremental diff + 7 from prior review)
Fix these issues in Kilo Cloud Previous review (commit 4b39fa6)Verdict: 2 Issues Found | Recommendation: Address before merge Overview
Issue Details (click to expand)
🏆 Best part: The previous P2 hardening feedback was actually taken seriously — 💀 Worst part: The new changes required fields but forgot to guard against empty strings. It's like installing a security door but leaving the key under the mat. 📊 Overall: Like a house that got a new roof but left the windows open — major progress, but the schema still leaks emptiness. Two quick Files Reviewed (1 changed file in incremental diff + 7 from prior review)
Fix these issues in Kilo Cloud Previous review (commit 768b31a)Verdict: No Issues Found | Recommendation: Merge Oh wait, this PR is actually clean. I need to sit down. I had my flamethrower warmed up and everything. 📊 Overall: Like finding a unicorn in production — I didn't think clean PRs existed anymore, but here we are. Files Reviewed (7 files)
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| "validation": { | ||
| "type": "array", |
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After the current schema requires type and result for validation items, "validation": [] still satisfies this required field because the array has no minItems. That lets extracted trajectory records pass without any CI/test/manual validation signal, which undermines the stated patch/fix → validation → outcome dataset step; add minItems: 1 here if every accepted record must include validation evidence.
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| "description": "GitHub repository in owner/repo form." | ||
| }, | ||
| "pr_number": { | ||
| "type": "integer", |
There was a problem hiding this comment.
For GitHub PR trajectories, pr_number must identify an actual pull request number, but this schema accepts 0 and negative integers. If an extractor emits one of those values, the record can pass validation while later provenance links or GitHub API lookups point to an impossible PR; add a minimum: 1 constraint here.
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| "before_context": { | ||
| "type": "string", |
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Because before_context is top-level required but only constrained to be a string, "before_context": "" still validates. That accepts trajectory records with no pre-change code/state snippet or file reference, breaking the repository's code state → patch/fix signal and making repair examples much harder to audit; add a non-empty constraint here.
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Caution
Some comments are outside the diff and can’t be posted inline due to platform limitations.
⚠️ Outside diff range comments (2)
schemas/pr_trajectory.schema.json (2)
19-22:⚠️ Potential issue | 🟡 Minor | ⚡ Quick winConstrain
pr_numberto valid PR IDs.Line 19 currently accepts
0and negative values, which are invalid PR numbers and can pollute downstream datasets.Proposed schema fix
"pr_number": { "type": "integer", + "minimum": 1, "description": "Pull request number within the repo." },🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@schemas/pr_trajectory.schema.json` around lines 19 - 22, The pr_number field in the schema currently has no minimum value constraint, allowing invalid PR numbers like 0 and negative values to pass validation. Add a minimum value constraint to the pr_number field definition to ensure only positive integers are accepted, specifically by adding a minimum property set to 1 to restrict pr_number to valid pull request identifiers.
69-81:⚠️ Potential issue | 🟡 Minor | ⚡ Quick winRequire at least one validation event.
Line 69 makes
validationrequired, but[]still passes. That weakens the trajectory contract for consumers expecting post-change verification evidence.Proposed schema fix
"validation": { "type": "array", + "minItems": 1, "items": { "type": "object",🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@schemas/pr_trajectory.schema.json` around lines 69 - 81, The validation array property is marked as required but currently allows an empty array, which defeats the purpose of enforcing post-change verification evidence. Add a minItems constraint set to 1 on the validation array definition to ensure at least one validation event object is always present when the validation property is included in the schema.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Outside diff comments:
In `@schemas/pr_trajectory.schema.json`:
- Around line 19-22: The pr_number field in the schema currently has no minimum
value constraint, allowing invalid PR numbers like 0 and negative values to pass
validation. Add a minimum value constraint to the pr_number field definition to
ensure only positive integers are accepted, specifically by adding a minimum
property set to 1 to restrict pr_number to valid pull request identifiers.
- Around line 69-81: The validation array property is marked as required but
currently allows an empty array, which defeats the purpose of enforcing
post-change verification evidence. Add a minItems constraint set to 1 on the
validation array definition to ensure at least one validation event object is
always present when the validation property is included in the schema.
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README.md (1)
52-52: LGTM!docs/data-policy.md (1)
51-53: LGTM!
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Fixed 1 file(s) based on 1 unresolved review comment. Co-authored-by: CodeRabbit <noreply@coderabbit.ai>
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Actionable comments posted: 2
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@schemas/pr_trajectory.schema.json`:
- Line 78: The required array in the validation items schema section currently
includes "detail" alongside "type" and "result", but based on your stated
intent, only "type" and "result" should be mandatory fields. Remove "detail"
from the required array so that the field becomes optional rather than enforced,
allowing validation events that don't need explanatory text (such as simple
automated results like "CI passed") to omit the detail field without forcing
placeholder values.
- Line 55: The required constraint in the review_signals schema definition
currently enforces all three fields (author, comment, and suggestion) as
mandatory. Locate the required array in the review_signals schema and remove
"suggestion" from the list to make it optional, keeping only "author" and
"comment" as required fields. This allows review signals to be captured even
when reviewers identify issues without providing specific actionable
suggestions.
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🔇 Additional comments (2)
schemas/pr_trajectory.schema.json (2)
1-45: LGTM!
60-101: LGTM!
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@schemas/pr_trajectory.schema.json`:
- Around line 55-58: The field definitions for author, comment, and suggestion
are not nested inside a properties object, causing invalid JSON schema syntax.
Wrap these three field definitions (author, comment, suggestion) inside a
properties object block, ensuring they are properly nested as key-value pairs
within the properties object. Then close the properties object with a closing
brace before the additionalProperties field. Apply the same fix to the detail
field at line 80 where the same nesting issue occurs.
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schemas/pr_trajectory.schema.json
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- GitHub Check: Kilo Code Review
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| "author": { "type": "string", "minLength": 1 }, | ||
| "comment": { "type": "string", "minLength": 1 }, | ||
| "suggestion": { "type": "string", "minLength": 1 } | ||
| "additionalProperties": false |
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As committed, this schema is not valid JSON: the author/comment/suggestion constraints are inserted after the nested properties object without forming a valid key/value sequence. Any validator or loader fails while parsing the schema before it can validate trajectory records, so the new schema cannot be used until these constraints are moved inside properties or the object syntax is repaired.
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Kilo agent: xAI/ Grok Build 0.1
All the new P2 points have been addressed:
pr_number: now has"minimum": 1before_context: now has"minLength": 1validation: now has"minItems": 1at the array level + required["type", "result"]on items (detail optional but has minLength when present)review_signalsitems: required only["comment"](suggestion is optional per CodeRabbit's own later suggestion to relax it; all three fields have minLength:1 to prevent empty strings).gitignore: removed thedatasets/jsonl/*.jsonlrule so small curated examples can be committed (as documented in datasets/README.md)
The schema was also fully rewritten to be valid JSON (previous autofix merges had introduced duplicate keys and fields outside the properties object — that was the critical parse error CodeRabbit flagged).
Schema on the branch is now clean and valid.
Pushed in the latest commits on this PR.
Happy to adjust further if needed.
| "properties": { | ||
| "author": { "type": "string" }, | ||
| "comment": { "type": "string" }, | ||
| "suggestion": { "type": "string" } |
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After the schema syntax is repaired, a review_signals item still only declares optional fields and has no required/anyOf constraint, so an extractor could emit review_signals: [{}] or an item with only author and still satisfy the item schema. That leaves records claiming review signal provenance without any actual review comment or suggestion for review-to-patch training; require at least comment or suggestion when an item is present.
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| # Keep the .gitkeep files tracked, ignore actual data | ||
| datasets/raw/* | ||
| !datasets/raw/.gitkeep | ||
| datasets/jsonl/*.jsonl |
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When someone tries to add a small curated JSONL trajectory under the documented datasets/jsonl/ location, this pattern hides it from normal git add/git status; I confirmed git check-ignore -v datasets/jsonl/sample.jsonl points here. That contradicts datasets/README.md's guidance that datasets/jsonl/ is for cleaned linked JSONL records with only small examples/schema samples/cards committed, and can cause validated records to remain local unless force-added or moved elsewhere.
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…ls and validation (Kilo: xAI/ Grok Build 0.1) - review_signals items: author, comment, suggestion now all have minLength:1 (addresses kilo-code-bot nitpick) - validation items: detail now has minLength:1 (addresses kilo-code-bot nitpick) Also fixed broken JSON syntax from previous merges (duplicate keys, missing commas) that was causing Biome parse failures in CodeRabbit. Cites: Kilo agent: xAI/ Grok Build 0.1 This should make the schema fully tight against empty strings in required fields. Refs PR #8 new comments from kilo-code-bot and CodeRabbit Biome warning.
…t P2s (Kilo: xAI/ Grok Build 0.1) - Create providers/ for external model/inference provider adapters and config (no weights) - Add providers/README.md documenting purpose and what does not belong - Update README layout to list providers/ - Fix schema if/then: add "required": ["training_use"] so conditional only applies when field present (kilo-code-bot) - Tighten repo pattern to reject impossible GitHub owner names (chatgpt-codex P2) - Make example self-consistent: repo/ci-demo#17, only matching source_url (chatgpt-codex P2) - Fix sample patch hunk ranges + minimal context (chatgpt-codex P2) Refs PR #8, closes remaining open review threads on this batch.
Five findings from the Codex review of 5a98c3c. Local agent/tracker state in curated patches (P1). PR #26's record embedded full diffs for .beads/ (config, git hooks, tracker exports) and .claude/settings.json — 12 of its 25 files. The .beads/issues.jsonl export carried a personal email in an `owner` field, so a curated artifact shipped contributor PII alongside machine-local config that docs/data-policy.md excludes. Extended `_is_noise_patch_path`, which already exists for exactly this, with a directory-prefix rule. Expected-failure cue still lacked intent (P1). The `failure behavior|mode|case|path|handling` alternative enclosed the only fail token in "CI showed failure behavior on Linux", inverting it to pass. Replaced with a deliberately-invalid-fixture cue, which is what PR #24 actually reads on; a bare failure noun is no longer a cue. Self-references from the raw record (P2). The guard only covered synthesized stubs, so a pre-collected same-repo issue matching the PR number survived into `seen` and out again. Now filtered on the way in. Copilot reviewer counted as CI (P2). `copilot-pull-request-reviewer` missed `_REVIEW_APP_CHECK_MARKERS`, so reviewer automation bolstered a passing CI result. Added the marker and moved it to review_apps. Stale indexes (P2). README called grok-ozempic "shortlist only" and STATUS listed the extraction as an open gap with the obsolete six-PR roadmap including dropped #8. PR #26 regenerated: patch_chars 67711 -> 50149, before_context file count 25 -> 13, manifest sha256/bytes updated. No other record changes.
* feat: grok-ozempic-v0 trajectories (revised 7-PR shortlist) Extracts the grok-ozempic v0 dataset for GH #11, with the shortlist re-scored against what the pipeline actually keeps rather than raw comment volume. Shortlist changes: - add #43 (quantize-goz1 CLI) and #33 (test refactor) — both fill the previously empty review-to-patch bucket; #33 also supplies the only refactor task_type in the set - drop #8: yields 2 review signals, one being "@copilot Make changes to the pull request" - defer #42: 51 kept signals collapse to 8 identical ack bodies, and it is Python against a Rust card with no language_by_pr override Measured by replaying every PR through lib/bots.is_bot_user and lib.normalize.extract_review_signals (cap 8). rmems is the repo's only human account, so most signal comes via the gemini/codex allowlist. Also adds a task_type override for #26, whose non-conventional title ("Verify grok-ozempic aligns...") fell through to "other" despite adding grok1_inventory.rs and alignment.rs. 7 records, all 8 review signals, quality 0.90-0.95, strict schema + policy validation clean. Raw records stay local per .gitignore. Refs #11 Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * fix(normalize): repair linked-issue provenance and expected-failure validation Addresses review findings on #17. Linked-issue provenance: - Drop self-referential linked issues. Issues and PRs share one number space, so a synthesized /issues/<pr> URL resolves back to the PR itself. This is what put issues/26 on the PR #26 record instead of real issue provenance. - Add LINKED_ISSUE_OVERRIDE for PR bodies that name their originating issue without a GitHub close keyword ("Implements GitHub #22", "for issues #16, #22, and #27", "addressing issues #28 and #20"). parse_linked_issue_numbers only recognises close keywords by design, so PRs #29/#33/#43 shipped with the PR URL as their only source. Expected-failure validation: - A negative-test line ("Manual invalid schema fixture confirms ingest failure behavior") matched the fail-word heuristic and stored PR #24's test result as `fail` despite every listed command and CI passing. Fail words are now checked per occurrence, so a deliberate failure no longer inverts the result while a real one alongside it still does. Dataset: source_urls corrected on records 26/29/33/43, PR #24 test result set to pass, manifest source_url_count/sha256/bytes regenerated. * fix(normalize): require explicit expected-failure markers; case-fold override keys Both findings from the Codex review of 3401a79. Expected-failure cue was too loose (P1). The reporting-verb alternative matched any of confirms/verified/checks/ensures followed by a fail word within 80 characters, so ordinary failure reports were inverted to `pass` — reproduced with "CI checks failed on Linux" and "Verified that cargo test failed". Every alternative now carries an explicit intentionality marker (expected/intended/intentional/deliberate, "fails as expected", failure behaviour|mode|case|path|handling, negative test). PR #24 still classifies as pass via "ingest failure behavior". Override keys are now case-folded (P2). GitHub repo slugs are case-insensitive but `parse_repo` preserves whatever the CLI was given, so collecting with `--repo RMEMS/GROK-OZEMPIC` missed every lookup in TASK_TYPE_OVERRIDE, DOMAIN_OVERRIDE, TRAINING_USE_OVERRIDE and the new LINKED_ISSUE_OVERRIDE — silently relabelling PR #26 and dropping the issue provenance just restored. All four tables now resolve through `_override_key`. Datasets are unchanged; both fixes are guarded by new regression tests. * fix: drop local agent config from patches; tighten expected-failure cue Five findings from the Codex review of 5a98c3c. Local agent/tracker state in curated patches (P1). PR #26's record embedded full diffs for .beads/ (config, git hooks, tracker exports) and .claude/settings.json — 12 of its 25 files. The .beads/issues.jsonl export carried a personal email in an `owner` field, so a curated artifact shipped contributor PII alongside machine-local config that docs/data-policy.md excludes. Extended `_is_noise_patch_path`, which already exists for exactly this, with a directory-prefix rule. Expected-failure cue still lacked intent (P1). The `failure behavior|mode|case|path|handling` alternative enclosed the only fail token in "CI showed failure behavior on Linux", inverting it to pass. Replaced with a deliberately-invalid-fixture cue, which is what PR #24 actually reads on; a bare failure noun is no longer a cue. Self-references from the raw record (P2). The guard only covered synthesized stubs, so a pre-collected same-repo issue matching the PR number survived into `seen` and out again. Now filtered on the way in. Copilot reviewer counted as CI (P2). `copilot-pull-request-reviewer` missed `_REVIEW_APP_CHECK_MARKERS`, so reviewer automation bolstered a passing CI result. Added the marker and moved it to review_apps. Stale indexes (P2). README called grok-ozempic "shortlist only" and STATUS listed the extraction as an open gap with the obsolete six-PR roadmap including dropped #8. PR #26 regenerated: patch_chars 67711 -> 50149, before_context file count 25 -> 13, manifest sha256/bytes updated. No other record changes. * fix(normalize): filter noise dirs in diff prefilter; require asserted intent Two P1s from the Codex review of 79191d7, both on code from that commit. The diff prefilter was basename-only. `_filter_noise_from_diff` returns early unless a `_NOISE_PATCH_BASENAMES` token appears in the text, so the new `_NOISE_PATCH_DIRS` rule never ran on the inline/sidecar path — the one the collector normally supplies. A diff touching only .beads/ or .claude/ files would have kept its hunks intact. PR #26 was filtered only because its .beads/.gitignore happens to contain the substring ".env". The prefilter now scans for directories as well as basenames. The fixture cue accepted a bad adjective as intent. "Invalid fixture was repaired, but cargo test failed on Linux" matched, because the gap between "fixture" and the fail word allowed any non-period characters and swallowed the clause boundary. The fixture must now be the subject of a confirming verb whose object is the failure (confirms/verifies/triggers/ demonstrates/shows/proves), with \w+ gaps that cannot cross a comma. PR #24 still classifies as pass on "invalid schema fixture confirms ingest failure behavior". Datasets are unchanged; both fixes affect future normalization only, and both are pinned by regression tests. * fix(normalize): nested agent state, exact copilot check, unmet expected failures Four findings from the Codex review of b6dd6ae. Nested agent state (P1). `_NOISE_PATCH_DIRS` was matched as a root prefix, so a monorepo's pkg/.claude/settings.json or workspace/.beads/config.yaml kept its hunk. Now matched as a path component, with `beads/` and `.beadsfoo/` still excluded. Copilot marker was a generic product term (P2). Substring "copilot" would also classify real CI such as "Copilot integration tests" as a review app, dropping it from ci_checks — and if it were the only successful check the record would report no validation evidence at all. Narrowed to the exact `copilot-pull-request-reviewer` check name. Expected failure that never happened (P2). "The invalid fixture was expected to fail, but it passed unexpectedly" describes a negative test that accepted input it should have rejected, but classified as pass. The cue proves intent, not that the failure occurred. A contradiction now forces `fail`. This one predates the expected-failure work — verified that disabling `_fail_words_all_expected` gives the same result — but it is a real gap in the same area. Also: `_fail_words_all_expected` returned True when a section had cue spans and no fail words at all, vacuously. Now False. Truncation inventory (P2). docs/source-repos.md claimed #11, #24 and #26 all truncate at the 96 KiB budget. Only #11 does and carries the footer; #24 (77,970) and #26 (50,149) are complete. Corrected, and noted that #26 is smaller than its raw diff because agent state is filtered. * fix(normalize): recognize absence-of-failure wording as a failed negative test Codex P2 on b4de520. The contradiction matcher added in that commit only covered `passed`/`succeeded` and the exact phrase `did not fail`, so "The expected failure did not occur" and "was not observed" still suppressed to pass — reproduced both. Generalized to absence wording: did not / does not / was not / were not / never, followed within two words by fail / occur / observed / seen / triggered / raised / reported / happen. The contradiction only applies when an expected-failure cue is also present, so ordinary resolved-failure prose ("previously failed tests are now passing") is unaffected — covered by the test alongside the new cases. PR #24 still classifies as pass. Datasets unchanged. * fix(normalize): scope expected-failure contradiction to a single sentence Codex P2 on a562309. The contradiction check tested the cue and the absence wording independently against the whole section, so an unrelated later clause matched: "Invalid fixture fails as expected. The warning did not occur" forced a passing validation to `fail`. Reproduced, along with the list-item form. `_expected_failure_was_contradicted` now splits on sentence boundaries and newlines and requires both to appear in the same part, so the contradiction must actually negate the failure it sits with. Same-sentence cases are unaffected. This one produced a false `fail` rather than a false `pass`, so no shipped record could have been inflated by it. Datasets unchanged; PR #24 still classifies as pass. * docs: align shortlist wording with closed_by_pr semantics; refresh STATUS date Two of four findings from the CodeRabbit review of a562309. The shortlist table said "Closes #22" for #26 and "Closes #16, #22, #27" for #29, but those numbers come from LINKED_ISSUE_OVERRIDE, whose stubs carry closed_by_pr: False precisely because the PR bodies use reference wording ("Implements GitHub #22"), not close keywords. The doc therefore contradicted the dataset it describes. Changed to "References", matching the "Advances" wording already used for the other override-backed rows. STATUS.md still read "Last updated: 2026-07-24" while recording the 2026-08-02 extraction. Also added the missing docstring on `_override_key`. The other two findings are not changes: the `.env.` prefilter token is already covered (".env" is a substring of ".env.production.local", so the prefilter fires and the file is filtered — verified), and review-signal dedupe is issue #18, deliberately deferred. Both answered on their threads. * fix(normalize): treat soft-wrapped lines as one statement Codex P2 on 6a59e9d, a regression from the sentence-scoping fix in 76ba370. Splitting on every newline broke Markdown soft wraps, so "The expected failure\nwas not observed" landed the cue and its contradiction in separate parts and the contradiction never fired — a false `pass`. Reproduced both wrapped forms. _SENTENCE_SPLIT now breaks only on real statement boundaries: sentence punctuation, a blank line, or the start of a list item. A bare newline is no longer a boundary. Both the wrapped forms and the genuine boundaries (sentence, list item, paragraph) are pinned by tests. Datasets unchanged; PR #24 still passes. * chore(ci): drop .gitlab-ci.yml The project builds on GitHub Actions; the GitLab pipeline duplicated the same lint/test/validate stages and had drifted — its validate stage ran `validate_jsonl.py` without `--strict-policy`, so it was a weaker gate than the GitHub one it mirrored. * docs: align #29 domain with the card; correct #33 review-density wording Two findings from the CodeRabbit review of 5f4d741. The shortlist table gave #29 a domain of "validation, CI" while both datasets/cards/grok-ozempic-v0.json (domain_by_pr) and the record itself say "validation" — the only row of the seven that disagreed. Dropped the ", CI"; the CI aspect is already carried by the Title ("Docker CI") and the Signal column ("Docker + cargo audit"), so nothing is lost. #33 was described as "highest human review density in the repo", but the measured table counts signals *after* the bot filter, and this section states rmems is the repo's only human account — most of those 70 kept signals are gemini/codex. Reworded to "highest filtered review-signal density", which is what was actually measured. * fix: strip linked Macroscope notes; allow modifiers in expected-failure cue Two findings from the Codex review of 695e068. Macroscope summaries were never stripped. `_MACROSCOPE_NOTE` required the literal phrase "Macroscope summarized", but the attribution renders as `<a href="...">Macroscope</a> summarized` — name and verb are not adjacent, so the pattern never matched. PR #24's validation event therefore carried the bot's entire change summary after its six real commands, truncated mid-footer at the 1500-char limit. The regex now tolerates markup between name and verb; record #24's test detail drops from 1504 chars to 358 and ends cleanly at its Closes list. Expected-failure cue required `expected` to sit immediately before the fail word, so "the expected test failure was observed" was recorded as a failed validation. Now allows up to two modifiers. Bounded deliberately: "We expected a clean run but saw 3 test failures" and "Not expected: the suite failed on main" both still classify as fail, and both are pinned. Manifest sha256/bytes regenerated. * fix(bots): scope Macroscope stripping to one note; revert cue widening Both findings from the Codex review of 2075610 were regressions in that same commit. The Macroscope pattern was destroying content. Its leading `.*?` reached forward for the attribution, so a PR body with a legitimate `[!NOTE]` before a later bot summary lost the human note *and* every validation line between them. Reproduced: human note and `cargo test` commands both vanished. Now matches one `> [!NOTE]` blockquote run at a time and drops it only when that block carries the attribution, mirroring how _GEMINI_IMPORTANT_BLOCK already works. The expected-failure cue widening is reverted. Allowing modifiers between the intent marker and the fail word let "The CI was expected to be failing on Linux until the runner is repaired" — a known-broken run — suppress to `pass`. That is the fabricating direction, so the round-9 improvement is not worth its cost; its test is removed with it. Known limitation, deliberately left: "intentionally failing on Windows" still suppresses to `pass`. Restricting the cue to negative-test subjects fixes it but then reads "expected to fail, but it passed unexpectedly" as `pass` instead. Measured both — every configuration retains exactly one false pass; only removing the heuristic has none. * fix(normalize): filter .kilo/ agent state; recognize asserted negative tests Two findings from the Codex review of 39a7a1a. .kilo/ was missing from _NOISE_PATCH_DIRS (P1), so a collected PR carrying local Kilo agent state would leak it into a curated patch — the same class as the .beads/ and .claude/ leak fixed earlier, which shipped a contributor email. This repo's own .codacy.yml already excludes .kilo/**, so the classification was settled, just not applied here. Near-misses `kilo/`, `.kilofoo/` and `src/kilo_backend.rs` stay unfiltered. The `negative test` cue only ever spanned those two words, so "Negative test confirms failure behavior" left the fail token outside any cue span and recorded a successful negative test as `fail`. Extended through an explicit observing/confirming verb — the same shape as the fixture alternative — rather than by loosening the intent marker, which is what produced last round's false pass. "Negative test suite reported 3 failures", "Negative tests failed on Windows" and "Negative test added. CI checks failed on Linux" all still classify as fail, and all three are pinned. Full 13-case matrix green. 75 tests, ruff clean, --strict-policy clean. * fix(bots): keep a separator when dropping a Macroscope note CodeRabbit finding on 2b7b340, and a real defect in the note-scoping fix from 39a7a1a. `_NOTE_BLOCK` consumes the newline preceding the block, so replacing an attributed block with "" spliced the line before the note onto the line after it. Reproduced: two distinct validation commands merged into - cargo test --features cli- invalid fixture confirms failure behavior Returns "\n" instead. Non-Macroscope blocks are still returned verbatim, so unattributed notes are untouched either way. The regression test asserts the surrounding lines survive as two separate entries, not just that the bot text is gone — the previous test passed while the splice was happening because it only checked for absence. --------- Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
Live gh scan dated 2026-08-16 across the extraction fleet: - corinth-canal: add Candidate next wave (#125-#128, #138, #142 with measured raw review counts; note the GH#147 safetensors series and the #126->#138 recovery pair) - grok-ozempic: add Candidate next wave (#69-#79 GOZ1 v2/v3 + expert remedies; flag #83 [112 reviews] and #86 beyond the wave) - limen-neural: refresh Later waves pointers with live numbers, note the Limen-Neural -> rmems transfers, add the remaining issue-#28 wave B repos (plasticity-lab, brainstem-daemon, synaptic-mesh, nir-rs) - new worktrees-hives.md shortlist (9 PRs; #61 80 rev / #65 60 / #63 53, plus the #88-#105 lab-CLI wave) - shortlist drafted - new theseus-quarry.md shortlist (7 of 9 merged PRs; #13 35 rev, #8 28, #9 17) - shortlist drafted - new wave-c.md rmems org pointer table for issue #29 repos - _index.md: Parked (Tier C) section; regenerate Index for the three new docs (build_status.py) Full wave B/C shortlists land when #28/#29 are decomposed. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* data: extract theseus-quarry-v0 telemetry trajectories Shortlist five merged PRs (#13, #9, #12, #11, #8). Defer #16 and #18. Per-PR domain and task_type labels live on the dataset card only. Co-authored-by: Raul Montoya Cardenas <montoyaraul34@gmail.com> * test: prove Theseus-Quarry domain_by_pr beats a planted DOMAIN_OVERRIDE Temporarily insert conflicting shared-dict rows for #8/#9/#12, assert the card still wins, then restore the table so the test stays isolated. Co-authored-by: Raul Montoya Cardenas <montoyaraul34@gmail.com> --------- Co-authored-by: Cursor Agent <cursoragent@cursor.com>
Fourth confirmed instance of the same pattern (neuromod #9, kinetic-signals #1): both retained review findings still describe defects present in the merged patch, with no corrective follow-up captured -- new_cortical() mixes absolute and relative voltage conventions the runtime kinetics don't handle, and reset() hard-codes resting state by temperature instead of deriving it from the neuron's own parameters. Recategorized repair -> bug-prediction via the card's training_use_buckets and synced both doc mirrors.
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User description
feat(scaffold): initialize project + schema v0 + data policy (GH #1/#2/#3)
Summary
Initial project scaffolding and foundational artifacts for Operation Prometheus.
models/directory created per instruction.schemas/pr_trajectory.schema.json(draft v0, not final)task_type,outcome,training_usedatasets/examples/trajectory-v0-example.jsondocs/data-policy.mdAlso adds support for using the global personal Beads DB (
raulmc-prefix) from this repo:.beads/README.mddocumentsBEADS_DIR=/home/raulmc/.beadsusage.gitignoreupdated to ignore.beads/*except the README (no local DB fragmentation)raulmc-vgeandraulmc-9cq(created, claimed, implemented, closed)Changes
Type of Change
Pre-flight Checklist
git statusclean before commitruff check,pytest -q, validate script placeholders)bd create,--claim,close)githubandgitlabremotes for testingTesting
feat/initialize-scaffoldRelated
feat/initialize-scaffoldThis is the foundation before any GitHub extraction scripts or larger datasets.
CodeAnt-AI Description
Set up the project structure and document the first trajectory data rules
What Changed
Impact
✅ Clearer dataset submission rules✅ Easier navigation of the repository✅ Safer public-data collection💡 Usage Guide
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