Bug 25387 [Wizards] [resources] File System Import changes file permissions
Creating a Project (simple or otherwise) and importing files into it using the import->File System wizard takes away the executable permission from the imported exec files.
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/wizards/datatransfer/ImportOperation.java
if (contentStream == null) {
            errorTable
                    .add(new Status(
                            IStatus.ERROR,
                            PlatformUI.PLUGIN_ID,
                            0,
                            NLS.bind(DataTransferMessages.ImportOperation_openStreamError, fileObjectPath),
                            null));
            return;
        }
        try {
            if (targetResource.exists())
                targetResource.setContents(contentStream,
                        IResource.KEEP_HISTORY, null);
            else
                targetResource.create(contentStream, false, null);
            
            if (provider instanceof TarLeveledStructureProvider) {
            	try {
            		targetResource.setResourceAttributes(((TarLeveledStructureProvider) provider).getResourceAttributes(fileObject));
            	} catch (CoreException e) {
            		errorTable.add(e.getStatus());
            	}
            }
        } catch (CoreException e) {
            errorTable.add(e.getStatus());
        } finally {
            try {
                contentStream.close();
            } catch (IOException e) {