more notes

Author: cscheid

.beads/issues.jsonl

@@ -467,6 +467,7 @@
 {"id":"k-67","title":"Update all parsing code to populate both source_info fields","description":"Update all parsing code across all modules to populate both source_info and source_info_qsm fields.\n\nFor each struct construction:\n- Keep existing source_info using pandoc::location::SourceInfo\n- Add source_info_qsm using node_to_source_info_with_context() from source_map_compat.rs\n\nThis ensures gradual migration without breaking existing code.\n\nFiles to update: All readers/treesitter/*.rs parsing modules","notes":"Current: 141 missing field errors. Sub-tasks created: k-72 through k-77. See phase3-sourceinfo-migration-guide.md","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-20T10:04:03.558959-05:00","updated_at":"2025-10-20T11:21:55.811406-05:00","closed_at":"2025-10-20T11:21:55.811406-05:00","dependencies":[{"issue_id":"k-67","depends_on_id":"k-65","type":"blocks","created_at":"2025-10-20T10:04:03.560757-05:00","created_by":"cscheid"},{"issue_id":"k-67","depends_on_id":"k-66","type":"blocks","created_at":"2025-10-20T10:04:03.561851-05:00","created_by":"cscheid"},{"issue_id":"k-67","depends_on_id":"k-63","type":"parent-child","created_at":"2025-10-20T10:04:03.564626-05:00","created_by":"cscheid"}]}
 {"id":"k-68","title":"Test that all source locations are preserved","description":"Verify that source location tracking works correctly after migration.\n\nTests:\n- Run existing test suite (all should pass)\n- Verify source_info_qsm fields are populated correctly\n- Spot check a few parsing modules to ensure locations match\n- Test inline location tracking\n- Test block location tracking\n\nThis validates the dual-field approach before switchover.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-20T10:04:10.636767-05:00","updated_at":"2025-10-20T11:26:25.717196-05:00","closed_at":"2025-10-20T11:26:25.717196-05:00","dependencies":[{"issue_id":"k-68","depends_on_id":"k-67","type":"blocks","created_at":"2025-10-20T10:04:10.638345-05:00","created_by":"cscheid"},{"issue_id":"k-68","depends_on_id":"k-63","type":"parent-child","created_at":"2025-10-20T10:04:10.639298-05:00","created_by":"cscheid"}]}
 {"id":"k-69","title":"Replace source_info with source_info_qsm throughout","description":"Final switchover from old to new SourceInfo type.\n\nTasks:\n- Remove 'pub source_info: SourceInfo' (pandoc::location) from all structs\n- Rename 'pub source_info_qsm' to 'pub source_info' everywhere\n- Update all field access from .source_info_qsm to .source_info\n- Update serialization derives if needed\n- This is the breaking change that completes the migration","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-20T10:04:18.15738-05:00","updated_at":"2025-10-20T12:52:21.024388-05:00","closed_at":"2025-10-20T12:52:21.024388-05:00","dependencies":[{"issue_id":"k-69","depends_on_id":"k-68","type":"blocks","created_at":"2025-10-20T10:04:18.158891-05:00","created_by":"cscheid"},{"issue_id":"k-69","depends_on_id":"k-63","type":"parent-child","created_at":"2025-10-20T10:04:18.159759-05:00","created_by":"cscheid"}]}
+{"id":"k-6daf","title":"Good source location tracking of document after engine outputs","description":"After engine execution (Jupyter, knitr, etc), the pipeline has two PandocAST structs: the pre-engine AST with source locations pointing to the original qmd, and the post-engine AST with locations pointing to intermediate engine output files. We need a tree-diffing algorithm to reconcile these ASTs, transferring original source locations to unchanged elements while keeping new locations for elements that changed (code execution outputs).\n\nPlan: claude-notes/plans/2025-12-15-engine-output-source-location-reconciliation.md\nRelated: claude-notes/plans/2025-12-15-source-info-for-structured-formats.md","status":"open","priority":1,"issue_type":"feature","created_at":"2025-12-15T15:53:21.187508-06:00","updated_at":"2025-12-15T15:54:35.598252-06:00"}
 {"id":"k-7","title":"Update postprocess function to use DiagnosticCollector","description":"Change postprocess function signature from generic ErrorCollector trait to concrete DiagnosticCollector type in src/pandoc/treesitter_utils/postprocess.rs","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-18T15:29:02.832735-05:00","updated_at":"2025-10-18T15:30:37.920982-05:00","closed_at":"2025-10-18T15:30:37.920982-05:00","dependencies":[{"issue_id":"k-7","depends_on_id":"k-12","type":"blocks","created_at":"2025-10-18T13:52:28.279485-05:00","created_by":"import"}]}
 {"id":"k-70","title":"Remove pandoc::location module","description":"Delete the old pandoc::location module after migration is complete.\n\nTasks:\n- Remove src/pandoc/location.rs file\n- Remove 'pub mod location;' from src/pandoc/mod.rs\n- Remove any remaining imports of pandoc::location types\n- Remove source_map_compat.rs (temporary bridge module)\n- Verify no references remain to old Location, Range, SourceInfo types\n- Run cargo check to ensure clean compilation","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-20T10:04:26.83249-05:00","updated_at":"2025-10-20T13:25:36.442096-05:00","closed_at":"2025-10-20T13:25:36.442096-05:00","dependencies":[{"issue_id":"k-70","depends_on_id":"k-69","type":"blocks","created_at":"2025-10-20T10:04:26.83385-05:00","created_by":"cscheid"},{"issue_id":"k-70","depends_on_id":"k-63","type":"parent-child","created_at":"2025-10-20T10:04:26.83474-05:00","created_by":"cscheid"}]}
 {"id":"k-71","title":"Run full test suite after migration complete","description":"Final validation that migration is complete and correct.\n\nTasks:\n- cargo test --package quarto-markdown-pandoc (all tests must pass)\n- cargo test --workspace (verify no breakage in other crates)\n- Verify all source location tracking still works\n- Check that error messages show correct locations\n- Document any remaining work or known issues\n\nSuccess criteria: All tests pass, no compilation errors, source tracking functional.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-20T10:04:34.574239-05:00","updated_at":"2025-10-20T15:01:18.681793-05:00","closed_at":"2025-10-20T15:01:18.681793-05:00","dependencies":[{"issue_id":"k-71","depends_on_id":"k-70","type":"blocks","created_at":"2025-10-20T10:04:34.5762-05:00","created_by":"cscheid"},{"issue_id":"k-71","depends_on_id":"k-63","type":"parent-child","created_at":"2025-10-20T10:04:34.577373-05:00","created_by":"cscheid"}]}
@@ -520,4 +521,5 @@
 {"id":"k-y2f3","title":"Add doctemplate support to quarto-markdown-pandoc","description":"Add document template support to quarto-markdown-pandoc with both bundle-based (for WASM) and filesystem-based (feature-gated) template resolution.\n\nPlan: claude-notes/plans/2025-12-05-doctemplate-integration.md\n\nKey components:\n1. MetaValue to TemplateValue conversion\n2. Template bundle format (JSON with main + partials)\n3. Library API with PartialResolver support  \n4. CLI integration (--template, --template-bundle)\n5. WASM entry points","status":"open","priority":1,"issue_type":"feature","created_at":"2025-12-05T11:14:01.283473-06:00","updated_at":"2025-12-05T11:14:58.723177-06:00"}
 {"id":"k-yvfo","title":"Conflict resolution for filesystem/automerge divergence","description":"Design what happens when: (1) hub starts and filesystem differs from stored automerge state, (2) external process modifies .qmd file while hub is running. Options: prefer filesystem, prefer automerge, merge, user prompt.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-08T13:24:58.012901-06:00","updated_at":"2025-12-08T13:24:58.012901-06:00","dependencies":[{"issue_id":"k-yvfo","depends_on_id":"k-4wex","type":"related","created_at":"2025-12-08T13:24:58.014686-06:00","created_by":"cscheid"}]}
 {"id":"k-z1ji","title":"Rename quarto-markdown-pandoc crate to pampa","description":"Rename the quarto-markdown-pandoc crate to 'pampa' as part of the project naming strategy. This includes renaming the directory, updating all Cargo.toml references, binary names, source imports, and documentation. See claude-notes/plans/2025-12-06-pampa-rename.md for detailed plan.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-06T14:44:48.188293-06:00","updated_at":"2025-12-06T15:01:18.104329-06:00","closed_at":"2025-12-06T15:01:18.104329-06:00"}
+{"id":"k-zr88","title":"Source information tracking for multiple surface syntax formats","description":"Design and implement source location tracking for structured input formats (ipynb, percent scripts) so that error messages can use the coordinate system of the original format (e.g., cell IDs + offsets) rather than positions in the converted qmd.\n\nPlan: claude-notes/plans/2025-12-15-source-info-for-structured-formats.md\nRelated design: claude-notes/surface-syntax-converter-design.md","status":"open","priority":2,"issue_type":"feature","created_at":"2025-12-15T13:41:27.074296-06:00","updated_at":"2025-12-15T14:13:07.621186-06:00"}
 {"id":"k-zvzm","title":"Design configuration merging system for pampa","description":"Design and document the Rust implementation of Quarto's mergeConfigs functionality. This involves studying existing code in quarto-yaml, pampa, and composable-validation, then proposing an architecture that supports !prefer/!concat tags, source location preservation, and efficient lazy/eager evaluation strategies.\n\nPlan file: claude-notes/plans/2025-12-07-config-merging-design.md","status":"in_progress","priority":1,"issue_type":"feature","created_at":"2025-12-07T09:25:04.943389-06:00","updated_at":"2025-12-07T09:30:16.359027-06:00"}