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Instead of doing three passes over the filesystem to collect source
files, it now does a single pass (using the newly introduced
FileUtils.listFiles) and later splits between .S, .c and .cpp files.
This allows sharing more code between the three file types and allows
removing Compiler.findFilesInFolder.
Additionally, this splits compileFiles into a version that compiles all
files in a folder and one that only compiles selected files. This
prepares for later refactoring of the Library class.
This has the side-effect of calling isAlreadyCompiled for .S files as
well (which didn't happen previously). However, since the assembler
command does not produce any .d files, .S files are still always
recompiled, just like before.
Finally, this has the side effect of handling file extensions in a case
insensitive manner during compilation (instead of just during load),
which means that e.g. .CPP files are not just loaded, but also compiled.
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