How to automatically configure Eclipse workspace

I want to know if there is some good way to automatically configure Eclipse workspace of newly checked out project.

I've got a project where I use gradle to both build and configure all of its subprojects. Since I want to enforce some good practices I also use e.g. FindBugs plugin, and tweaked Eclipse configuration (more/better compiler warnings, formatting, favorites, save actions and so on).

I think that storing .metadata directory in git is not a good idea - a lot of settings works only for certain version and breaks after update, some settings are stored in binary files and so on.

Build-in import/export tool handles only some settings - AFAIK it leaves e.g. save actions, favorites and formatting alone and don't handle them.

Then there's Workspace Mechanic plugin that allows to record settings change - but it doesn't allow to update existing record, only create new file or override old one, which leaves me with a lot of tasks to run - and it's not bug free: several times file_export_version=3.0 line was placed in a wrong place, so some settings couldn't be imported until I fixed that manually, and few times after import installation stopped working correctly... (even though I imported settings that I just exported!).

Do you have some good, automated, portable solution? Perhaps some tweaked way of using already mentioned tools? It might be more complicated that just running one script - I just want to make sure that all of changes are applied, I didn't miss anything, I don't have to change each and every option manually and it will still work when I apply it to an upgraded Eclipse.