Q:

Is eclipse.ini used for Java apps I compile and start from Eclipse or for the IDE itself? 

I read the articles on the following web sites but don't yet have a clear picture of the purpose of eclipse.ini:

https://wiki.eclipse.org/FAQ_How_do_I_increase_the_heap_size_available_to_Eclipse%3F,
https://wiki.eclipse.org/Eclipse.ini. 

My question is in the title. 

A:

The eclipse.ini file is just for Eclipse itself. 
For Java programs you run from Eclipse the configuration is in the 'Run > Run Configurations' dialog.