pca -> epca; file name extension changes and som functionality implemented. Still debugging.
guppy epca should now only write out as many components as are necessary when it needs to compute more than it needs to write out (basically for the case of doing 2-d rotations, where my implementation uses a 3d rotational matrix for unifromity of implementationd)
3d rotations working.
Cleaning up comments
Merged in pca-filtering branch
Cleaned up multimin: reduced start input copying; naming more consistent with rest of file; maximum number of iterations
Fixed a couple of som bugs; also put in more dynamic minimization tolerances
Cleaning up style related stuff
Have tests set up, but seemingly not being run yet. Seeking help from Aaron on this.
Fixing/running the Test_som suite.
Tests now passing; also, wider bounding box for 3d minimization routine and associated reordering of vars and trans when variance order becomes non-monotomic
Cleaned up minimization error handling and extra start_finder modularity and robustness for dealing with likelihood functions vs the less well behaved but easier to compute overlaps
Have minimization doing jumps around the raw start now. Was hoping this would entirely fix getting the signage of the rotated component vectors to match up the orignals as closely as possible, but seems like there is a little more work to do there.
Have SOM rotations manually ensuring that the rotated vectors are flipped so that the support signs (pos or neg) match as much as possible
comments
comments and minor tweaks
Merge 'dev' into 221-som-rotations compiles...

Conflicts:
	pplacer_src/guppy_pca.ml
	pplacer_src/minimization.ml
New version of 3D rotation, checked w/ Mathematica
Comments and tweaks.
Index fix; more descriptive var names.