you can specify the workspace locn at startup (with -d iirc) so with an alias and/or some bash scripting you can use a separate workspace for each project (I have my projects in ~/proj as subdirs with commands to select which is current - although I only use eclipse for c dev work, intellij idea for java + python).

also, use a separate build tool (eg ant) and don't store build info in eclipse (basically, use as default a config as possible and "import from" the build tool). then if you do need to start from scratch you lose very little (and don't add the eclipse metadata to git).