Presumably the source included the TTF files from which the rasterized bitmap resources were automatically generated. Including the pre-rasterized bitmaps extracted from a previous release should not be a problem as typefaces and bitmap fonts are not subject to copyright in the US, vs vector font files which are eligible for copyright as computer programs.
The Bluetooth stack, except for a stub that will function in an emulator
This seems unfortunate, and looks to be one of the most critical gaps in the source release.
The STM peripheral library
You can get this from ST no problem, although it is only licensed for use on STM devices.
The voice codec
It should be feasible enough to replace this.
ARM CMSIS
The old versions with non-free licenses are still available from ARM or ST, and the recent versions are Apache licensed (but some porting of code might be required to use to newer versions).
For the Pebble 2 HR, the heart rate monitor driver
This was probably based on sample code from the vendor which could be replaced.
