v1.0.1

v1.0.1 — Reproducibility, CI, and API curation

A maintenance and infrastructure release: gated continuous-integration test
lanes, deterministic identity/fingerprinting primitives, MCP integration docs,
a curated public API surface, and targeted fixes. It builds on the v1.0.0
two-layer toolbox without changing its workflows.

Testing & continuous integration

• Authoritative test-suite builder (buildSuite) and a runCI gate that runs
  the headless, UI, clean-process, and quick lanes and fails on Failed or
  Incomplete tests.
• runQuickTests now returns a pass flag and errors on failure when no output
  is captured, so it can act as a gate.
• Manual GitHub Actions workflow (workflow_dispatch) running the quick and
  identity lanes, including cross-platform matrix jobs.
• Golden-file regression fixtures and notes under tests/golden/.

Identity & reproducibility primitives (+pf2_base/+identity/)

• Deterministic canonical byte encoding, domain-separated (named) hashing, and
  SHA-256 digests.
• A tagged JSON/MAT transport for round-tripping values canonically.
• Source and imported-data fingerprinting, plus a fail-closed expected-digest
  preflight that gates importers.

Processing methods

• Shipped Takizawa oxy seed methods (takizawa_easy / takizawa_hard, lenient
  and strict automatic channel rejection — Takizawa et al. 2008) added to the
  default library.
• Method reference tables and examples updated to the live registry and to the
  OD_TDDR raw method.

Public API & namespace curation

• The Context processing option now uses the public pf2.ProcessingContext;
  the public fromRecipe helper was removed.
• Method-authoring internals moved out of the primary pf2.* surface into
  pf2_base: seed factories and discovery to pf2_base.methods.seeds,
  function-metadata validation to pf2_base.methods.validateFunction, the
  add/edit-function tools to pf2_base.methods.functions, and the tutorial
  demo-pipeline setup to pf2_base.examples.addDemoPipelines.
• Retired the pf2.GUI.configureRawMethods / configureOxyMethods /
  functions wrappers; the supported method editors are
  pf2.methods.raw.configureMethods and pf2.methods.oxy.configureMethods.

MCP integration

• mcp/README.md and mcp/TOOL_CARD.md: how to drive processFNIRS2 from an MCP
  client through the MATLAB MCP Server.

Documentation

• pf2_sSMART header references added (Curtin & Ayaz 2019; Ayaz et al. 2010 for
  the SMAR detection stage) and an expanded Notes section on the DC-offset
  (ShiftCorrect) correction and its caveats; pf2_functions_default.cfg
  argument list, role, defaults, and parameter metadata corrected to match the
  function.
• Docs clarify pf2_base as an advanced-and-internal package.

Fixes

• getTakizawaRejection now uses the first FFT bin above 1 Hz as a scalar index
  rather than the full index vector.
• Signed-zero handling: negative zero round-trips canonically as +0 through
  the JSON transport, with explicit test coverage.

Full Changelog: v1.0.0...v1.0.1