Dev

.agents/skills/protocol-migration/SKILL.md

@@ -1,75 +1,113 @@
 ---
 name: protocol-migration
-description: Convert legacy/source.txt into README.md using the repository template, preserving scientific meaning and marking uncertainty with CHECK:.
+description: Convert legacy/source.md into README.md using the repository template, using source.txt only as fallback and marking uncertainty with CHECK:.
 ---
 
 Use this skill when migrating a legacy protocol into this repository template.
 
 Goal:
-Convert `legacy/source.txt` into `README.md`, using the existing `README.md` as the target template and structure.
+Convert `legacy/source.md` into `README.md`, using the existing `README.md` as the target template and structure.
 
-Primary sources:
-- `legacy/source.txt` is the main source
-- also consult the PDF in `legacy/` for tables, layout-dependent content, and anything unclear
+## Primary rule
+Do not change protocol meaning.
+Use `legacy/source.md` as the primary source when rewriting `README.md`.
+Use `legacy/source.txt` only as a fallback when `legacy/source.md` looks malformed, incomplete, or unclear.
+Use the PDF file in `legacy/` as the final reference source of truth for tables, figures, layout-dependent content, and anything still ambiguous.
+If `legacy/source.md` and `legacy/source.txt` disagree, prefer `legacy/source.md` for general structure and prose, but use the original PDF as the final tie-breaker.
 
-Core rules:
-- Do not change protocol meaning
-- Do not invent missing information
-- Do not delete source content
-- Do not silently summarize, compress, or merge steps
-- Preserve exact reagent names, quantities, timings, temperatures, and conditions unless only formatting is being normalized
-- Preserve step order unless the source clearly indicates otherwise
-- If anything is uncertain, mark it with `CHECK:` instead of guessing
+## Migration behavior
+When converting legacy protocol content into the repository template:
 
-If content does not fit cleanly:
-- place it under `# Migration notes` or `## Unplaced content`
+- Preserve all protocol content.
+- Preserve all procedural content, warnings, notes, reagent names, quantities, timings, temperatures, and conditions, preserving their location.
+- Do not change scientific meaning.
+- Do not invent missing information.
+- Do not invent missing values or steps.
+- Do not delete any content from the source.
+- Do not silently summarize, compress, or merge steps.
+- Keep exact reagent names, quantities, temperatures, timings, and conditions unless only formatting is being normalized.
+- Preserve exact reagent and equipment names unless only formatting is changing.
+- Preserve the step order from the source unless the source clearly indicates otherwise.
+- Do not delete repeated warnings or notes.
+- If any text does not fit cleanly into the template, place it under `# Migration notes` or `## Unplaced content`.
+- Mark uncertainty with `CHECK:` instead of guessing.
 
-Allowed formatting normalization only when meaning is unchanged:
-- add a space between numbers and units
-- standardize temperature formatting to `37 °C`
-- standardize volumes to `µL`, `mL`, `L`
-- standardize concentrations to `mM`, `µM`, `nM`, `% (w/v)`
-- standardize time units to `seconds`, `minutes`, `hours`
-- standardize pH formatting to `pH 7.4`
-- normalize bullets, headings, and markdown tables to match the template
-- use tables for reaction mixes and other tabular content
-- use HTML subscripts for chemical formulas where needed
-- normalize note-like text to blockquote style, e.g. `> **Note**`
+## Allowed formatting normalization
+You may normalize formatting only when the meaning is unchanged and unambiguous:
 
-Do not:
-- infer omitted values
-- replace vague wording like `overnight` or `room temperature` with precise values
-- reorder steps unless clearly justified by the source
-- remove repeated warnings or notes
-- replace one reagent with another
-- omit unmapped text
+- Add a space between numbers and units.
+- Standardize temperature formatting to `37 °C`.
+- Standardize volume units to `µL`, `mL`, `L`, using the micro sign `µ` consistently.
+- Standardize concentration units to `mM`, `µM`, `nM`, `% (w/v)`, etc., using the micro sign `µ` consistently.
+- Standardize time units to full words: `seconds`, `minutes`, `hours`.
+- Standardize chemical names to match the source but with consistent formatting (e.g. `Tris-HCl` instead of `Tris HCl`).
+- Standardize pH formatting to `pH 7.4`.
+- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
+- Do not use Unicode subscript characters such as `₂`.
+- Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
+- Normalize bullet formatting and markdown table formatting.
+- Normalize heading structure to match the repository template.
+- For reaction mixes and anything tabular, place them inside a table as in template.
+- Normalize markdown headings, bullets, and tables.
+- "Note" or "NOTE" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- Remove empty columns from tables.
+- Synchronize `Contents` with actual headings in the protocol.
 
-Output requirements:
+## Disallowed changes
+- Do not infer omitted concentrations, times, temperatures, or volumes.
+- Do not infer values for missing quantities.
+- Do not try to calculate or infer values that are not explicitly stated.
+- Do not convert `overnight`, `RT`, `briefly`, `room temperature` or similar vague language into precise values.
+- Do not replace vague language with precise values.
+- Do not reorder steps unless the source clearly numbers them in that order.
+- Do not remove duplicate-looking content unless it is truly identical and both copies are preserved in review notes.
+- Do not rewrite scientific wording for style if that risks changing meaning.
+- Do not fill in table cells with values that are missing from the source.
+- Do not replace one reagent name with another.
+- Do not remove repeated warnings or notes.
+- Do not omit unmapped text.
+
+## Output requirements
 - edit `README.md`
-- use the template headings
-- keep the template badge at the top
-- remove the template instruction note
+- use the template headings exactly
+- use the template headings in `README.md`
+- keep all source content
+- add `CHECK:` markers for uncertainty
+- use `CHECK:` only for genuine unresolved uncertainty. If no uncertainty remains, do not mention `CHECK:` at all
+- add `# Migration notes`
+- after drafting, add a short summary in `# Migration notes` covering:
+  - formatting normalizations performed
+  - ambiguities and uncertainty flagged
+  - content placed in `## Unplaced content`
 - add `# Migration notes` including:
   - imported protocol metadata from `source-metadata.yml` if present
+  - imported protocol metadata from `source-metadata.yml` using only the non-blank lines
   - template metadata from `template-metadata.yml`
   - ambiguous mappings
-  - formatting normalizations performed
+  - normalized formatting changes
   - content copied verbatim but not confidently placed
+- keep the template badge at the top
+- keep ![Created with ulelab Protocol Template](https://img.shields.io/badge/created%20with-ulelab%20Protocol%20Template-blue) at the top of the file
+- remove the template instruction note
+- delete the "Template repository: Click `Use this template` to create a new protocol repo..." note
 
+## Verification
 After drafting, verify the migration against the source:
-- compare the migrated `README.md` against `legacy/source.txt`
-- - compare the migrated `README.md` against the PDF in `legacy/`
+- compare the migrated `README.md` against `legacy/source.md`
+- compare any malformed, incomplete, or ambiguous passages against `legacy/source.txt`
+- compare the migrated `README.md` against the PDF in `legacy/` for tables, figures, layout-dependent content, and any remaining ambiguity
 - check that all protocol steps, notes, warnings, reagent names, quantities, temperatures, timings, and conditions are still present
 - check that no source content has been silently omitted, merged, or reordered without justification
 - check any tables, layout-dependent content, or ambiguous sections against the PDF in `legacy/`
 - leave `CHECK:` anywhere the mapping is uncertain rather than guessing
 
 Verification checklist:
-- `README.md` still matches the scientific content of `legacy/source.txt`
+- `README.md` still matches the scientific content of `legacy/source.md`
+- any malformed, incomplete, or ambiguous passages were cross-checked against `legacy/source.txt`
 - no protocol steps or warnings were omitted
 - no values were invented or made more precise than in the source
 - tables and layout-dependent content were checked against the PDF in `legacy/`
 - any uncertain mappings are marked with `CHECK:`
 - any meaningful normalization choices are noted in `# Migration notes`
 
-Prefer preserving meaning over making the output prettier.
+Prefer preserving meaning over making the output prettier.

.claude/.claude/skills/protocol-migration/SKILL.md

@@ -1,75 +1,113 @@
 ---
 name: protocol-migration
-description: Convert legacy/source.txt into README.md using the repository template, preserving scientific meaning and marking uncertainty with CHECK:.
+description: Convert legacy/source.md into README.md using the repository template, using source.txt only as fallback and marking uncertainty with CHECK:.
 ---
 
 Use this skill when migrating a legacy protocol into this repository template.
 
 Goal:
-Convert `legacy/source.txt` into `README.md`, using the existing `README.md` as the target template and structure.
+Convert `legacy/source.md` into `README.md`, using the existing `README.md` as the target template and structure.
 
-Primary sources:
-- `legacy/source.txt` is the main source
-- also consult the PDF in `legacy/` for tables, layout-dependent content, and anything unclear
+## Primary rule
+Do not change protocol meaning.
+Use `legacy/source.md` as the primary source when rewriting `README.md`.
+Use `legacy/source.txt` only as a fallback when `legacy/source.md` looks malformed, incomplete, or unclear.
+Use the PDF file in `legacy/` as the final reference source of truth for tables, figures, layout-dependent content, and anything still ambiguous.
+If `legacy/source.md` and `legacy/source.txt` disagree, prefer `legacy/source.md` for general structure and prose, but use the original PDF as the final tie-breaker.
 
-Core rules:
-- Do not change protocol meaning
-- Do not invent missing information
-- Do not delete source content
-- Do not silently summarize, compress, or merge steps
-- Preserve exact reagent names, quantities, timings, temperatures, and conditions unless only formatting is being normalized
-- Preserve step order unless the source clearly indicates otherwise
-- If anything is uncertain, mark it with `CHECK:` instead of guessing
+## Migration behavior
+When converting legacy protocol content into the repository template:
 
-If content does not fit cleanly:
-- place it under `# Migration notes` or `## Unplaced content`
+- Preserve all protocol content.
+- Preserve all procedural content, warnings, notes, reagent names, quantities, timings, temperatures, and conditions, preserving their location.
+- Do not change scientific meaning.
+- Do not invent missing information.
+- Do not invent missing values or steps.
+- Do not delete any content from the source.
+- Do not silently summarize, compress, or merge steps.
+- Keep exact reagent names, quantities, temperatures, timings, and conditions unless only formatting is being normalized.
+- Preserve exact reagent and equipment names unless only formatting is changing.
+- Preserve the step order from the source unless the source clearly indicates otherwise.
+- Do not delete repeated warnings or notes.
+- If any text does not fit cleanly into the template, place it under `# Migration notes` or `## Unplaced content`.
+- Mark uncertainty with `CHECK:` instead of guessing.
 
-Allowed formatting normalization only when meaning is unchanged:
-- add a space between numbers and units
-- standardize temperature formatting to `37 °C`
-- standardize volumes to `µL`, `mL`, `L`
-- standardize concentrations to `mM`, `µM`, `nM`, `% (w/v)`
-- standardize time units to `seconds`, `minutes`, `hours`
-- standardize pH formatting to `pH 7.4`
-- normalize bullets, headings, and markdown tables to match the template
-- use tables for reaction mixes and other tabular content
-- use HTML subscripts for chemical formulas where needed
-- normalize note-like text to blockquote style, e.g. `> **Note**`
+## Allowed formatting normalization
+You may normalize formatting only when the meaning is unchanged and unambiguous:
 
-Do not:
-- infer omitted values
-- replace vague wording like `overnight` or `room temperature` with precise values
-- reorder steps unless clearly justified by the source
-- remove repeated warnings or notes
-- replace one reagent with another
-- omit unmapped text
+- Add a space between numbers and units.
+- Standardize temperature formatting to `37 °C`.
+- Standardize volume units to `µL`, `mL`, `L`, using the micro sign `µ` consistently.
+- Standardize concentration units to `mM`, `µM`, `nM`, `% (w/v)`, etc., using the micro sign `µ` consistently.
+- Standardize time units to full words: `seconds`, `minutes`, `hours`.
+- Standardize chemical names to match the source but with consistent formatting (e.g. `Tris-HCl` instead of `Tris HCl`).
+- Standardize pH formatting to `pH 7.4`.
+- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
+- Do not use Unicode subscript characters such as `₂`.
+- Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
+- Normalize bullet formatting and markdown table formatting.
+- Normalize heading structure to match the repository template.
+- For reaction mixes and anything tabular, place them inside a table as in template.
+- Normalize markdown headings, bullets, and tables.
+- "Note" or "NOTE" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- Remove empty columns from tables.
+- Synchronize `Contents` with actual headings in the protocol.
 
-Output requirements:
+## Disallowed changes
+- Do not infer omitted concentrations, times, temperatures, or volumes.
+- Do not infer values for missing quantities.
+- Do not try to calculate or infer values that are not explicitly stated.
+- Do not convert `overnight`, `RT`, `briefly`, `room temperature` or similar vague language into precise values.
+- Do not replace vague language with precise values.
+- Do not reorder steps unless the source clearly numbers them in that order.
+- Do not remove duplicate-looking content unless it is truly identical and both copies are preserved in review notes.
+- Do not rewrite scientific wording for style if that risks changing meaning.
+- Do not fill in table cells with values that are missing from the source.
+- Do not replace one reagent name with another.
+- Do not remove repeated warnings or notes.
+- Do not omit unmapped text.
+
+## Output requirements
 - edit `README.md`
-- use the template headings
-- keep the template badge at the top
-- remove the template instruction note
+- use the template headings exactly
+- use the template headings in `README.md`
+- keep all source content
+- add `CHECK:` markers for uncertainty
+- use `CHECK:` only for genuine unresolved uncertainty. If no uncertainty remains, do not mention `CHECK:` at all
+- add `# Migration notes`
+- after drafting, add a short summary in `# Migration notes` covering:
+  - formatting normalizations performed
+  - ambiguities and uncertainty flagged
+  - content placed in `## Unplaced content`
 - add `# Migration notes` including:
   - imported protocol metadata from `source-metadata.yml` if present
+  - imported protocol metadata from `source-metadata.yml` using only the non-blank lines
   - template metadata from `template-metadata.yml`
   - ambiguous mappings
-  - formatting normalizations performed
+  - normalized formatting changes
   - content copied verbatim but not confidently placed
+- keep the template badge at the top
+- keep ![Created with ulelab Protocol Template](https://img.shields.io/badge/created%20with-ulelab%20Protocol%20Template-blue) at the top of the file
+- remove the template instruction note
+- delete the "Template repository: Click `Use this template` to create a new protocol repo..." note
 
+## Verification
 After drafting, verify the migration against the source:
-- compare the migrated `README.md` against `legacy/source.txt`
-- - compare the migrated `README.md` against the PDF in `legacy/`
+- compare the migrated `README.md` against `legacy/source.md`
+- compare any malformed, incomplete, or ambiguous passages against `legacy/source.txt`
+- compare the migrated `README.md` against the PDF in `legacy/` for tables, figures, layout-dependent content, and any remaining ambiguity
 - check that all protocol steps, notes, warnings, reagent names, quantities, temperatures, timings, and conditions are still present
 - check that no source content has been silently omitted, merged, or reordered without justification
 - check any tables, layout-dependent content, or ambiguous sections against the PDF in `legacy/`
 - leave `CHECK:` anywhere the mapping is uncertain rather than guessing
 
 Verification checklist:
-- `README.md` still matches the scientific content of `legacy/source.txt`
+- `README.md` still matches the scientific content of `legacy/source.md`
+- any malformed, incomplete, or ambiguous passages were cross-checked against `legacy/source.txt`
 - no protocol steps or warnings were omitted
 - no values were invented or made more precise than in the source
 - tables and layout-dependent content were checked against the PDF in `legacy/`
 - any uncertain mappings are marked with `CHECK:`
 - any meaningful normalization choices are noted in `# Migration notes`
 
-Prefer preserving meaning over making the output prettier.
+Prefer preserving meaning over making the output prettier.