The journal's input requirements are very straightforward.
To fix ideas, let's assume that your document consists of four files you created yourself: main.tex, sec1.tex, sec2.tex, and mybib.bib. mybib.bib may contain entries that are not cited in the body of the document. Let's also assume that you know to deploy \cite, \bibliographystyle, and \bibliography statements and that you know how and when to run BibTeX, in addition to LaTeX, in order to create the formatted bibliography (which will be stored in main.bbl).
Suppose, next, that main.tex has the following structure:
\documentclass{<whatever>} % does the journal specify which document class must be used?
% preamble material, including a suitable \bibliographystyle instruction
\begin{document}
\input sec1 % including various \cite directives
\input sec2
\bibliography{mybib}
\end{document}
The first applicable instruction is:
Prepare only one .tex file; do not use \include or \input to incorporate another source file.
To meet this requirement, simply delete (or comment out) the two \input statements in main.tex and replace them with the contents of sec1.tex and sec2.tex. After these operations, main.tex should contain the complete LaTeX code for the document.
The only way this can fail is if the final pdf file consists of -- in addition to files with extension .tex -- graphics files (in eps, png, or pdf format, say) that are loaded via \includegraphics statements. If the final pdf file does rely on externally-stored graphics files, you'll simply have to include them alongside main.tex when you upload the files to the journal's website.
The second instruction is:
If you are using BibTeX, do not submit .bib and .bbl files. Instead, compile your LaTeX and copy the contents of the generated .bbl file into your .tex file.
After running LaTeX, BibTeX, and LaTeX twice more to create the formatted bibliography and resolve all \cite commands, delete (or comment out) the \bibliography statement and replace that statement with the contents of main.bbl. These contents will likely start with \begin{thebibliography}{<some integer>} and end with \end{thebibliography}.
You should be able to compile the complete file main.tex with LaTeX without any further ado. It is this version of main.tex that you should submit to the journal.
Some final comments: It's actually quite striking that the journal doesn't appear to impose any additional requirements regarding the document class, the font families, or the page layout. Consider yourself lucky! Do make life for the journal's editorial team as simple as possible by using either article or report as the document class and only the standard font families, and do make sure to engage in very little or, better still, no visual formatting. The editorial team will take note and be most appreciative.
Best Answer
Short version: I would put the BIB files to
~/texmf/bibtex/bib/myfiles/myfile.biband style files to~/texmf/tex/latex/myfiles/myfile.styfor example.Long version: try
which will show you where you can put your local files, so that TeX will find them out-of-the-box. By default this is
~/texmf(for your personal files) and/usr/local/texlive/texmf-local(for system-wide additions). Inside that tree you need to follow TDS standard. For BIB files that would be:That is default value in TeX Live 2011 at least. You may check
texmf.cnfon your system if the value is any different, or try to run one of the following commands:This will tell you where BibTeX searches for BIB files.
If you need those files only for a couple of projects and/or don't want to pollute your home folder, the cheapest trick is to create a TDS structure anywhere on the disk and only set
TEXMFHOMEto point to that location.Setting
TEXINPUTSandBIBINPUTSis not recommended. SettingPATHonly helps you to find binaries likepdftex, but thenpdftexshould be able to findtexmf.cnfand that file contains enough information to find everything else. You can override any setting fromtexmf.cnfwith environmental variables, but I would suggest you to place the files to locations where TeX expects them as opposed to setting variables.