After a little bit of playing around these are the steps I figured out. I'm currently using Eclipse Helios with Android NDK r6b.
- Remove the lib and jni folders from your project and delete the contents of the bin folder.
- From Windows Explorer remove the .cproject file and .externalToolBuilders folder if either of them exist in your project's root folder.
- Edit the .project file in your project's root folder and remove any lines that match the following.
Look for the following in between the buildSpec tags:
andorg.eclipse.cdt.managedbuilder.core.genmakebuilder clean,full,incremental, ?children? ?name?=outputEntries\|?children?=?name?=entry\\\\\\\|\\\|\|| ?name? org.eclipse.cdt.make.core.append_environment true org.eclipse.cdt.make.core.buildArguments E:\dev\android\android-ndk-r6b\ndk-build org.eclipse.cdt.make.core.buildCommand bash org.eclipse.cdt.make.core.cleanBuildTarget clean org.eclipse.cdt.make.core.contents org.eclipse.cdt.make.core.activeConfigSettings org.eclipse.cdt.make.core.enableAutoBuild false org.eclipse.cdt.make.core.enableCleanBuild true org.eclipse.cdt.make.core.enableFullBuild true org.eclipse.cdt.make.core.fullBuildTarget V=1 org.eclipse.cdt.make.core.stopOnError true org.eclipse.cdt.make.core.useDefaultBuildCmd false
Look for the following in between the natures tags:org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder full,incremental, org.eclipse.cdt.core.cnature org.eclipse.cdt.core.ccnature org.eclipse.cdt.managedbuilder.core.managedBuildNature org.eclipse.cdt.managedbuilder.core.ScannerConfigNature - Delete your project from your Eclipse workspace (but don't select the delete the files on disk option) and then re-import from the same directory.