Add documentation suite, license, and preprint citation

[Copilot]

Adds comprehensive documentation infrastructure for the AD_PAC MEG analysis pipeline and establishes proper attribution for the associated preprint (https://www.medrxiv.org/content/10.64898/2026.02.06.26345635v1).

Documentation Structure

Root-level (7 files, ~1.5K lines):

• README.md - Project overview, installation, complete pipeline usage
• CITATION.md - Preprint citation with BibTeX for paper and dependencies
• LICENSE - MIT License
• REQUIREMENTS.md - Dependency installation (MATLAB, FieldTrip, Brainstorm, FreeSurfer)
• QUICKSTART.md - Rapid onboarding guide with timeline estimates
• CONTRIBUTING.md - Contribution workflow and code of conduct
• CHANGELOG.md - Version history

Module-level (5 files):
Each pipeline stage (HeadModelling/, PreProcessing/, SourceReconstruction/, Pac/, Stat/) now includes detailed README covering:

• Function-level API documentation
• Configuration parameters and expected runtimes
• Quality control procedures
• Troubleshooting guides
• Advanced usage patterns

Key Features

• Preprint citation prominently displayed in README header and CITATION.md
• Installation verification checklists and test procedures
• Performance optimization guidance (parallel processing, batch strategies)
• Reproducibility details for all pipeline stages
• .gitignore configured to exclude large data files and results

Example Usage Flow

% Setup
main_path = '/path/to/AD_PAC/';
addpath(genpath(main_path));
addpath('/path/to/fieldtrip/'); ft_defaults;

% Pipeline stages (documented in detail)
anatomyTransform;          % ~1-5 min/subject
buildHeadModels;           % ~30-120 min/subject  
preprocessing;             % ~5-10 min/subject
sourceReconstruction_p;    % ~15-40 min/subject
seedRoitoCortex;          % ~30-90 min/subject
clusterBasedModel;        % Group-level statistics

Documentation provides complete coverage from installation through publication-ready analysis.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• www.medrxiv.org
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

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[Erfan7bt]

Documentation added by copilot. Reviewed and confirmed.