Organizing The Repository #68
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…g them in the root directory of the repo.
… the main web page (http://weizhongli-lab.org/cd-hit/) and some basic instructions on how to use cd-hit.
As of today, C++ source code files are named *.cpp and C++ Headers are usually named *.h. There is no good reason to keep using legacy file extensions such as ".c++" or ".cxx". The .c++ extension can cause problems on some file systems that don't allow the "+" character in file names.
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This project truly deserves a clean, well organized and good looking repository.
I moved source code files to a "src" directory and modified the Makefiles to write the binaries into a "bin" directory (a standard used by most projects). A ".gitignore" was added in order to prevent binary files being staged on commits.
The README file was also lacking more useful information, so I wrote one based on the previous file and the cd-hit web page.