files can be uploaded to a theme. Some of these have special meaning and for others it is the best place to store if used on all pages, eg, a page header logo. The special files used depends on the template, currently all templates use the same special files.
Special files:
style sheet
Any file MIME type "text/css" or suffix ".css" is added as a style sheet. multiple style sheets can be added, the order is set by the upload's rank. This/these style sheets are used in addition to and potentially override or extend the default style sheet which (on current templates) is always added first.
scripts
Any file MIME type "application/javascript" or suffix ".js" is added as a script file. multiple script files can be added, the order is set by the upload's rank.
favicon.ico
Any file MIME type "image/x-icon" or suffix ".ico" is added as an icon. multiple icons can be added but don't because it makes no sense. [TBD: add to theme check.] PNG icons are not supported. [TBD: why not "favicon.png"?]
apple-touch-icon.png
Any file with the name "apple-touch-icon.png" is added as, yes, an apple-touch-icon. This uses the name of the file not the MIME as it it type "image/png". [TBD: other sizes?] Current trends recommend this is a 57x57 PNG image.