Fixed issue with file extensions and CpGAT refrprot documentation

[standage]

This pull request addresses two issues I encountered trying to get the xGDBvm GUI to recognize the reference protein file I had saved in the appropriate directory.

• First, the documentation was inconsistent about whether the file should go in ~/xgdbvm/referenceprotein/ or ~/referenceprotein/. Perhaps a vestige of previous versions? Either way, I corrected the documentation to point to the correct folder. But even when I had my refrprot file in both folders, the config GUI didn't pick up on it, which leads to the second issue.
• As with many input files, xGDBvm was expecting the reference protein sequence file to have a specific filename extension: .fa in this case. My file had an .faa extension, which is common but unsupported in this case. This particular requirement is undocumented (unless I missed something), but rather than document it I chose instead to relax the requirement: I made a simple addition to the code in question (which looks like it's probably used elsewhere) to support .fa, .faa, .fsa, and .fasta as valid extensions.

Also, the addition to the .gitignore file is for temporary files created by Vim.

[standage]

Ok, well the extensions aren't something I have strong opinions on. So if in your experience strictness is warranted, I'd be happy to roll back the changes to XGDB/conf/conf_functions.inc.php and simply document the requirement of a .fa extension.

[standage]

Ok, I rolled back the changes to extension handling and documented the fact that reference protein files must have an .fa extension. It looks like you replaced examples/refpep/cegma_core.fasta with examples/referenceprotein/cegma_core.fa, presumably for the sake of the consistency which you just described, but did not remove the original file. I removed the old copy of the file, and replaced all references to it in the code with references the new file.