# =============================================================================
# Raw imaging data — NEVER track in git (TB on the lab drive)
# =============================================================================
*.tif
*.tiff
*.dv
*.dv.tiff
*.nd2
*.lsm
*.h5
*.ics
*.ids
*.czi
*.oif
*.oib
*.avi
*.mov
*.mp4
*.zip            # ROI sets, etc.

# =============================================================================
# R intermediates and rendered output (regenerated from source)
# =============================================================================
*.RData
*.rds
*.nb.html
*.html
.Rhistory
.Rapp.history
.Rproj.user/
*.Rcheck/
.Rprofile

# Output products — regenerated by knitting
outputs/
plots/

# =============================================================================
# Plot exports — re-rendered from source on demand
# =============================================================================
*.pdf
*.eps
*.svg
*.ps
# Allow specific docs/PDFs by exception:
!docs/**/*.pdf

# =============================================================================
# Python / Jython
# =============================================================================
__pycache__/
*.pyc
*.pyo
.venv/
venv/
.python-version

# =============================================================================
# MATLAB
# =============================================================================
*.asv
*.mat
slprj/

# =============================================================================
# Editor / IDE / OS junk
# =============================================================================
.DS_Store
Thumbs.db
desktop.ini
._*              # macOS resource forks
*.swp
*.swo
.idea/
.vscode/
*.sublime-*

# Agent / sync-tool runtime state — never publish (contains tool errors,
# subagent tracking, mission state, replay logs).
.omc/
**/.omc/

# =============================================================================
# User-local config / environment
# =============================================================================
config.local.yml
.env
.env.local
.Renviron

# =============================================================================
# Source data + manuscript artefacts (Nature owns post-acceptance)
# =============================================================================
SourceData/
KW_Dunn_*
*.docx
*.doc
*.pzfx
*.prism
*.xlsx
*.xls

# =============================================================================
# figures/EDFig10_em/ — selective publication (2026-05-08 reorganization).
# This directory used to be external_or_em_matlab/ but was folded into the
# regular figures/ track. Publication scope per the lead author:
#   - PUBLISHED with Florian Fassler attribution: the 3 Python helpers
#     (color_model.py, color_model_batch.py, object_mod.py) — annotated for
#     beginners on 2026-05-08; see CONTRIBUTORS.md.
#   - PUBLISHED: actin_fila_quant__*.rmd R Markdown documentation wrappers.
#   - NOT PUBLISHED: MATLAB filament-tracking scripts (.m) and TOM Toolbox
#     utilities (kept locally only, for internal reproducibility).
#   - NOT PUBLISHED: acpype.py (1.2 MB external MD force-field tool, not part
#     of the manuscript's analysis pipeline).
# Note: 4 non-Fassler files (combine.py, tilta_sirt-014.py, histplot.py,
# histplotgui.py) were REMOVED 2026-05-08 — they were either IMOD-generated
# boilerplate or generic Python 2 plot helpers.
# =============================================================================
figures/EDFig10_em/*.m
figures/EDFig10_em/**/*.m
figures/EDFig10_em/Matlab_scripts/
figures/EDFig10_em/tom_*.m
figures/EDFig10_em/acpype.py

# =============================================================================
# Build artefacts (the build/ scripts themselves stay tracked as audit trail)
# =============================================================================
build/*.log
build/cache/

# =============================================================================
# Per user 2026-05-13 (revised): keep only README.md, LICENSE, CITATION.cff,
# CONTRIBUTORS.md at the GitHub root. All audit-trail AND auxiliary user-facing
# files stay local only. The Zenodo deposit mirrors GitHub, so these are
# excluded from both. They remain on the maintainer's local disk so the
# build/ scripts (rename_log refresh, hash verification, panel-audit cascade)
# keep working.
# =============================================================================
/rename_log.csv
/hash_inventory.csv
/hash_groups.csv
/def_scan_audit.csv
/code_organization_plan.md
/panel_audit_*.md
/CLAUDE.md
/unused_scripts/
/build/
/env/
/config.yml
/figure_index.csv
/source_data_audit.md
/REDISTRIBUTION_NOTES.md
