> I got rid of most of the files in the autoload directory as Davide  
> had suggested in another thread.
Note that this will disable those features, so you need to be careful  
not to use them.  But if your input is TeX rather than MathML, you  
won't need most of them.  The important ones for TeX are mtable.js and  
multiline.js (if you are using automatic line breaks), and maction.js  
and menclose.js if you use the extensions that call on those (e.g.,  
the cancel extension needs menclose).
> Also, I have the config directory that contains the singleton tex- 
> ams_html.js file. Not sure why you got rid of the entire config  
> directory. When is that directory used anyway?
Tom has already indicated that it is the config=filename that causes  
these to load.  You can also add a config array to your configuration  
that would cause files from this directory to load.  The combined  
configuration files contain copies of the compressed code that is also  
in the jax and extensions directories, so if you use the combined  
configuration file, you can remove the originals.  But for local  
access in an app, there probably is not much advantage in that (it  
helps for network access, but not really for local file access).  So I  
think Tom's approach of putting the in-line configuration that loads  
the jax and extensions individually is probably best.  Then the config  
directory can be removed entirely, as he has done.
> You have couple of extra directories off \jax\output\html-css\fonts 
> \tex . Davide had mentioned that you could delete directories greek,  
> size1, size2, size3, size4, winie6. Not sure about the typewriter.
Typewriter is for the \tt font.  If you don't use that, you can remove  
it.  The Greek and WinIE6 directories are only for IE, so you won't  
need those.  If you don't use \cal, \frak, \sf, or \scr you can get  
rid of the Caligraphic, Fraktur, SanSerif, and Script directories as  
well (and can remove the corresponding OTF fonts).  But if you forget  
and try to use these, you will get errors, as there is no way to tell  
MathJax that these files are not there.
> Also, I would like to know if i can delete \jax\output\html-css\fonts 
> \tex\stix font directory.
I don't know if you can install STIX on Android or iOS, but if not,  
then sure, go ahead.  If you want to force the use of MathJax fonts  
even if STIX is available, then remove the directory, but be sure to  
configure  availableFonts: ["TeX"] so that MathJax won't try to use  
STIX fonts.
Davide