Allow libraries/sketches to have the same name as system libs,
e.g. main or Wire

Doesn't seem to work with main.cpp but main.ino works.

Fixes issue #229 and #244
Added *.cpp to extensions supported by "make generate_assembly"
Merge pull request #245 from sej7278/master

Allow libraries/sketches to have the same name as system libs. Fix #229 Fix #244