There are also files that are created by LaTeX2e, the .aux file, the .toc file and the .bib file. The .aux (auxiliary) file is where LaTeX stores all the information about the counters (like section numbers), footnotes, bibliography entries, reference marks, and anything else that LaTeX may need to keep track of. This file is written over whenever a file is typeset by LaTeX. Whenever a document is typeset LaTeX reads this file to get the information it need, and writes to it after typesetting is completed. This is why changes in the counters will not take effect until LaTeX is run twice, because the .aux file is not up to date the first time. The .bib file is where all the bibliography information is kept. You can either make this file yourself, or you can use BibTeX to create the file. The .toc file contains all the information needed to create the Table of Contents. This file is created when LaTeX sees the command \tableofcontents, and the section names, numbers and page numbers are all read from the .aux file.
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