Precursor info: I'm on a Mac operating OSX 10.9.4, which I updated to months ago, before this problem started. I'm running LyX 2.1.
Just a few days ago I was using LyX with no problems. The next day, error messages started popping up such as:
"The selected document class Article (Standard Class) requires external files that are not available. The document class can still be used, but the document cannot be compiled until the following prerequisites are installed: article.cls"
"The module linguistics requires a package that is not available in your LaTeX installation, or a converter that you have not installed. LaTeX ouptut may not be possible. Missing prerequisites: covington.sty"
"The module natbib requires a package that is not available in your LaTeX installation, or a converter that you have not installed. LaTeX ouptut may not be possible. Missing prerequisites: natbib.sty"
I also cannot access any of my .bib documents. When I go to Tools > TeX Information, nothing is there (i.e. the LaTeX classes and styles, and BibTeX styles and databases sections are all empty).
I do, however, have what I believe is the correct directory available:
username/Library/texmf/bibtex/bib/.bib_docs_here username/Library/texmf/bibtex/bst/.bst_docs_here username/Library/texmf/tex/latex/packages_&_styles_here
Things I've tried:
Tools > Reconfigure, then quitting and restarting LyX.
I was on LyX 2.0 when this started. I erased LyX 2.0 from my computer and installed LyX 2.1. At Library/Application Support/LyX-2.1/ there is the same texmf file there, so it does look like the installation of LyX 2.1 correctly copied all of that information.
Full computer restart.
Removing and replacing all TeX related folders in Library.
I'd very much appreciate any diagnoses of what the problem might be and/or advice on how to solve it. Thank you.