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TODO.md
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plans/done/refactor-columns-extract-to-use-tabulate.md
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plans/done/review-skill-70-readable-pipeline-scripts.md
plans/done/run-and-report-stderr-fix.md
plans/done/selection-to-frame-loops-and-tags-refactor.md
plans/done/streamfitter-data-preprocessing.md
plans/done/typical-column-ordering.md
plans/done/value-spec-dataclass.md
plans/done/value-spec-ergonomics-force-auto-loop-mix-stderr-fix.md
plans/outdated/mcp-subprocess-improvements.md
plans/outdated/old-mcp-sandbox.md
references/NEF_specification_paper_bioarchiv_April_2026.pdf
references/NEF_specification_paper_supplementary_bioarchiv_April_2026.pdf
references/Nmr Experiment Nomenclature v2.docx
references/fogh.vrankenj.bio.nmr.2006.36.147.pdf
references/kosol idps molecules-18-10802.pdf
scripts/check_circular.py
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src/nef_pipelines/lib/spectra_lib.py
src/nef_pipelines/lib/structures.py
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src/nef_pipelines/resources/preamble.md
src/nef_pipelines/resources/mcp_server/cli-idioms - NEF-Pipelines CLI common idioms and patterns.md
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src/nef_pipelines/resources/mcp_server/nef-nmr-data-model - NEF Molecular Structure and NMR Data Model.md
src/nef_pipelines/resources/mcp_server/readme - README for the NEF-Pipelines MCP server.md
src/nef_pipelines/resources/mcp_server/skill - index of available expert workflow skills.md
src/nef_pipelines/resources/mcp_server/skills - index of available expert workflow skills.md
src/nef_pipelines/resources/mcp_server/star-file-format - STAR format reference - read before working with NEF files .md
src/nef_pipelines/resources/mcp_server/skill/01-nef-pipelines-howto - how to use the NEF-Pipelines commands in a pipeline.md
src/nef_pipelines/resources/mcp_server/skill/02-adhoc-data -  Adhoc frame, loop and column creation from columnar files when no specific transcoder exists.md
src/nef_pipelines/resources/mcp_server/skill/70-writing-readable-pipeline-scripts - Conventions for converting pipeline invocations into human readable shell scripts.md
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src/nef_pipelines/transcoders/mars/importers/__init__.py
src/nef_pipelines/transcoders/mars/importers/peaks.py
src/nef_pipelines/transcoders/mars/importers/sequence.py
src/nef_pipelines/transcoders/mars/importers/shifts.py
src/nef_pipelines/transcoders/modelfree/__init__.py
src/nef_pipelines/transcoders/modelfree/exporters/data.py
src/nef_pipelines/transcoders/nmrpipe/__init__.py
src/nef_pipelines/transcoders/nmrpipe/nmrpipe_lib.py
src/nef_pipelines/transcoders/nmrpipe/peak_file_format.txt
src/nef_pipelines/transcoders/nmrpipe/importers/__init__.py
src/nef_pipelines/transcoders/nmrpipe/importers/peaks.py
src/nef_pipelines/transcoders/nmrpipe/importers/sequence.py
src/nef_pipelines/transcoders/nmrpipe/importers/shifts.py
src/nef_pipelines/transcoders/nmrstar/__init__.py
src/nef_pipelines/transcoders/nmrstar/nmrstar_lib.py
src/nef_pipelines/transcoders/nmrstar/importers/__init__.py
src/nef_pipelines/transcoders/nmrstar/importers/project.py
src/nef_pipelines/transcoders/nmrstar/importers/project_cli.py
src/nef_pipelines/transcoders/nmrstar/importers/project_shortcuts.py
src/nef_pipelines/transcoders/nmrstar/importers/rdcs.py
src/nef_pipelines/transcoders/nmrstar/importers/sequence.py
src/nef_pipelines/transcoders/nmrstar/importers/shifts.py
src/nef_pipelines/transcoders/nmrview/__init__.py
src/nef_pipelines/transcoders/nmrview/nmrview_lib.py
src/nef_pipelines/transcoders/nmrview/exporters/peaks.py
src/nef_pipelines/transcoders/nmrview/exporters/sequences.py
src/nef_pipelines/transcoders/nmrview/exporters/shifts.py
src/nef_pipelines/transcoders/nmrview/importers/__init__.py
src/nef_pipelines/transcoders/nmrview/importers/peaks.py
src/nef_pipelines/transcoders/nmrview/importers/sequence.py
src/nef_pipelines/transcoders/nmrview/importers/shifts.py
src/nef_pipelines/transcoders/pales/__init__.py
src/nef_pipelines/transcoders/pales/exporters/rdcs.py
src/nef_pipelines/transcoders/pales/exporters/template.py
src/nef_pipelines/transcoders/pales/importers/rdcs.py
src/nef_pipelines/transcoders/rcsb/__init__.py
src/nef_pipelines/transcoders/rcsb/align.py
src/nef_pipelines/transcoders/rcsb/rcsb_lib.py
src/nef_pipelines/transcoders/rcsb/trim.py
src/nef_pipelines/transcoders/rcsb/importers/sequence.py
src/nef_pipelines/transcoders/rpf/__init__.py
src/nef_pipelines/transcoders/rpf/exporters/__init__.py
src/nef_pipelines/transcoders/rpf/exporters/shifts.py
src/nef_pipelines/transcoders/shiftx2/__init__.py
src/nef_pipelines/transcoders/shiftx2/importers/shifts.py
src/nef_pipelines/transcoders/shifty/__init__.py
src/nef_pipelines/transcoders/shifty/exporters/__init__.py
src/nef_pipelines/transcoders/shifty/exporters/shifts.py
src/nef_pipelines/transcoders/sparky/__init__.py
src/nef_pipelines/transcoders/sparky/sparky_lib.py
src/nef_pipelines/transcoders/sparky/exporters/__init__.py
src/nef_pipelines/transcoders/sparky/exporters/peaks.py
src/nef_pipelines/transcoders/sparky/exporters/shifts.py
src/nef_pipelines/transcoders/sparky/importers/__init__.py
src/nef_pipelines/transcoders/sparky/importers/peaks.py
src/nef_pipelines/transcoders/sparky/importers/sequence.py
src/nef_pipelines/transcoders/sparky/importers/shifts.py
src/nef_pipelines/transcoders/talos/__init__.py
src/nef_pipelines/transcoders/talos/talos_lib.py
src/nef_pipelines/transcoders/talos/exporters/__init__.py
src/nef_pipelines/transcoders/talos/exporters/shifts.py
src/nef_pipelines/transcoders/talos/importers/__init__.py
src/nef_pipelines/transcoders/talos/importers/order_parameters.py
src/nef_pipelines/transcoders/talos/importers/restraints.py
src/nef_pipelines/transcoders/talos/importers/secondary_structure.py
src/nef_pipelines/transcoders/talos/importers/sequence.py
src/nef_pipelines/transcoders/ucbshift/__init__.py
src/nef_pipelines/transcoders/ucbshift/ucbshift_lib.py
src/nef_pipelines/transcoders/ucbshift/importers/__init__.py
src/nef_pipelines/transcoders/ucbshift/importers/sequence.py
src/nef_pipelines/transcoders/ucbshift/importers/shifts.py
src/nef_pipelines/transcoders/xcamshift/__init__.py
src/nef_pipelines/transcoders/xcamshift/exporters/__init__.py
src/nef_pipelines/transcoders/xcamshift/exporters/shifts.py
src/nef_pipelines/transcoders/xeasy/__init__.py
src/nef_pipelines/transcoders/xeasy/xeasy_lib.py
src/nef_pipelines/transcoders/xeasy/importers/peaks.py
src/nef_pipelines/transcoders/xeasy/importers/sequence.py
src/nef_pipelines/transcoders/xeasy/importers/shifts.py
src/nef_pipelines/transcoders/xplor/__init__.py
src/nef_pipelines/transcoders/xplor/psf_lib.py
src/nef_pipelines/transcoders/xplor/xplor_lib.py
src/nef_pipelines/transcoders/xplor/exporters/__init__.py
src/nef_pipelines/transcoders/xplor/exporters/rdcs.py
src/nef_pipelines/transcoders/xplor/importers/__init__.py
src/nef_pipelines/transcoders/xplor/importers/dihedrals.py
src/nef_pipelines/transcoders/xplor/importers/distances.py
src/nef_pipelines/transcoders/xplor/importers/sequence.py
tutorials/HowToManipulateDataWithNEFPipelines.pptx