I have a checked-out version of the Redmine-Mylyn connector open-source project. There are eight Eclipse plug-in projects plus two Eclipse features projects plus .git/ as their sibling in the local file system. It turns out that after importing them as Plug-ins and Fragments (with options Projects with source folders) Eclipse recognizes all plug-in projects but net.sf.redmine_mylyn in the Git repository (i.e. it shows a corresponding suffix next to these project names in its Project Explorer view.)
So net.sf.redmine_mylyn is apparently not recognized with these apparent effects: it has no such suffix in the Project Explorer view and its Team menu list only Apply Patch ... (but no other option related to either Git or sharing). However, if I run git status from the command line e.g. on net.sf.redmine_mylyn/build.properties I can see that it very well also part of the same repository. The Project Explorer does not show the two feature projects at all.
What could be the reason that Eclipse (Kepler) apparently does not recognize one plug-in project in the Git repository and how could I make it do so?
UPDATE
Here is how the .project files are arranged in the file system (output from find . -name .project):
./net.sf.redmine_mylyn/.project
./net.sf.redmine_mylyn.api/.project
./net.sf.redmine_mylyn.api-test/.project
./net.sf.redmine_mylyn.common/.project
./net.sf.redmine_mylyn.core/.project
./net.sf.redmine_mylyn.core-test/.project
./net.sf.redmine_mylyn.core.extension.timesheet_extensions_plugin/.project
./net.sf.redmine_mylyn.extensions.feature/.project
./net.sf.redmine_mylyn.feature/.project
./net.sf.redmine_mylyn.ui/.project
The .project files reference three or four buildCommands (org.eclipse.jdt.core.javabuilder, org.eclipse.pde.ManifestBuilder, org.eclipse.pde.SchemaBuilder, org.eclipse.pde.ds.core.builder)
and two natures (org.eclipse.pde.PluginNature, org.eclipse.jdt.core.javanature). The offending project is one of those which do not reference org.eclipse.pde.ds.core.builder.
And find . -name .git gives:
./.git
Using the usual Import > Existing Projects into Workspace wizard, I could not reproduce the problem. I don't know what Import > Plug-ins and Fragments is supposed to do, but it looks like a bug in there.
I recommend filing a bug for Eclipse PDE and add the link to it here. Be sure to include the specifics such as which repository you used. A high quality bug report contains: A series of steps to reproduce the problem (like you would write in a short tutorial), followed by "this is what I expected to happend" and "this is what actually happened".