Refactored and tested in string.cpp: IsValidIdentifier, ShortenVarID, toNum, Sort
Removed orphaned method declaration from StringBuffer
Merge branch 'v3-template' of github.com:veg/hyphy into v3-template

Because he said so
Commented out CString on its way to removal.
Removed old CStrings depricated code

Made the remaining global functions properly formatted free
functions.
Deleted remaining free functions from sequence

They don't appear to be used by anything.
Removed sequence.cpp from cmake file.
Merge pull request #197 from mdsmith/v3-template

V3 template
Finished unit testing and confirming functionality

Much of the old code is ready to be removed.
Merge branch 'v3-template' of github.com:veg/hyphy into v3-template

Updating branch before finishing refactoring and pushing changes.
Finished cleaning, confirmed coverage
Moved the methods peeled from the site class

Put them in site_helpers
Updated cpp file intro text
Attaching unit test file
Cleaning unit test file
Merge branch 'v3-template' of https://github.com/veg/hyphy into v3-template
Merge pull request #198 from mdsmith/v3-template

Site class refactoring
Merge branch 'v3-template' of https://github.com/veg/hyphy into v3-template
Removed some global functions and variables from the string class into hy_globals; started work in space methods
Tests for space functions; worked on FirstNonSpaceIndex and FirstSpaceIndex, but incomplete (tests fail)