Mark a file in the GIT repo as temporarily ignored

You are probably looking for

git update-index --assume-unchanged .project

If you need a common base for those (.project, .classpath, ...), you can:

• version template version of those files (.project_tpl, .classpath_tpl, ...)
• use a filter driver to generate, on checkout, the actual files (which won't be versioned, and only modified locally by the developers)

(the 'clean' step during commit wouldn't do anything for those templates.
Only the 'smudge' step is used here, to generate the private files)

Note: this is a slight "mis-use" of a filter driver, which is supposed to process only file contents, not to generate new ones.
But it could help you in your scenario (provided your 'smudge' script doesn't overwrite blindly the eclipse files if they happen to already be here.)