Rapidtide

* (rapidtide) Properly initialize "starttime" so that it will use the value in a json file, if present.
* (rapidtide) Added new option to start from a random probe regressor.
* (rapidtide) Moved performance options into their own section.
* (rapidtide) Cleaned up code that reads (or rereads) data prior to GLM.
* (rapidtide) You can specify MKL threads AND multiprocessing - multithreading is disabled and reenabled automatically as needed.
* (rapidtide) Do refinement on padded data, to infer data past the ends of the imaging window.
* (rapidtide) Save the padded, lagged timecourse generator.
* (rapidtide) Scale voxel timecourses prior to PCA refinement.
* (rapidtide) Change default refinement options.
* (rapidtide) Started to increase the granularity of output file specification.
* (fit) Added routines to do automated component selection from scree tests.
* (package) Updated all calls to np.polyfit to the new Polynomial class.
* (package) Merged some dependabot PRs.
* (package) Made pyfftw an optional dependency.
* (package) Fixed numba crashes (on Intel - not tested on ARM yet) and made it an optional dependency.
* (package) Made compatible with Python 3.12.

* (rapidtide) Spatial filtering with the default kernel (1/2 the average voxel dimension) is now the default.
* (rapidtide) Rewrote the lag time rank order calculation to use scipy.signal.rankdata.
* (rapidtide) Moved some command line options to the "experimental" section, where they should have been to begin with.
* (rapidtide) Moved GLM options to a new "GLM" section.
* (rapidtide) Do not automatically disable windowing for linear correlation.
* (rapidtide, happy) Reorganized, expanded and rationalized confound regression code.
* (tidepool) Replaced the flame colormap option with plasma and jet with turbo (similar, to what they replaced, but perceptually uniform).
* (package) Made some proactive fixes for numpy 2.0.0 compatibility.
* (package) Merged some dependabot PRs.
* (tests) Removed some superfluous metadata from test data files.
* (docs) Further extensive revisions.

* (rapidtide) Tweaked the behavior of the ``--CVR`` flag.
* (rapidtide) Made major improvements to motion regression.
* (rapidtide) Consolodated all glm filtering into a single multiprocessing routine, added some new capabilities to rapidtide GLM filtering.
* (resampletc) Renamed from resamp1tc to make the program names more consistent.
* (package) Made pyfftw an optional dependency, since it seems to be the only thing blocking python 3.12 compatibility.
* (package) Added some new tests.
* (package) Major reorganization of most scripts to make them workflows (this is to make the calling interfaces and documentation consistent.)
* (package) Incorporated dependabot changes.
* (docs) Further cleanup of the program documentation section, especially rapidtide usage.
* (docs) Expanded the Theory of Operation section.
* (docs) Fixed many typos.

* (docs) Extensive revision of the rapidtide program usage section.

* (rapidtide) Adjusted some default parameters to reflect the current best picks.
* (rapidtide) Fixed the --denoising option (it didn't actually do anything!)
* (package) Partially implemented a major reorganization of all the programs in the package to make them workflows with standard interfaces.
* (docs) Started the process of standardizing the program descriptions and properly using autodoc.

* (rapidtide) Output some .json sidecars that I had neglected.
* (glmsim) New program to help develop instructional tools re: how rapidtide works. This is a WIP.
* (docs) Major revisions to the rapidtide usage instructions.
* (package) Accepted several dependabot changes.