I recently upgraded from Eclipse Kepler to Luna. A plugin I had been working on is now showing build errors without any source being changed.
Here is an extract from my MANIFEST.MF,
Require-Bundle: org.eclipse.core.runtime;bundle-version="3.7.0",
org.eclipse.ui;bundle-version="3.7.0",
org.eclipse.ui.ide;bundle-version="3.7.0",
org.eclipse.core.resources;bundle-version="3.7.0",
org.eclipse.ui.forms;bundle-version="3.6.0",
org.eclipse.wst.sse.ui;bundle-version="1.3.0",
org.eclipse.jface.text;bundle-version="3.8.100",
org.eclipse.ui.workbench.texteditor;bundle-version="3.8.101",
org.eclipse.ui.views;bundle-version="3.6.0"
None of the core or ui bundles are resolved. I don't think Eclipse could even run without them and their equivalent .jar files are present and readable and haven't been modified as part of the upgrade, so they are not actually missing. When I try to add dependencies on the Dependencies tab the problem bundles do not show.
Eclipse was upgraded by the Arch Linux package manager. I mention it for completeness but believe it is likely identical to any other upgrade mechanism. I also tried creating a new plug-in project but the same happens, I guess this means it's a global setting. I'm relatively new to PDE and so far haven't had a need to change any settings.
From the preference page (Preferences > Plug-in Development > Target Platform), try Removing the Running Platform target definition, Applying, and then Restoring Defaults. Maybe it's just stale and pointing to the jars that it doesn't know Arch has changed about.