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
IPath sourceRootPath = null;
        if (this.source != null) {
            sourceRootPath = new Path(provider.getFullPath(this.source));
        }
        while (sourceIter.hasNext()) {
            Object nextSource = sourceIter.next();
            IPath sourcePath = new Path(provider.getFullPath(nextSource));
            IPath newDestinationPath;
            IResource newDestination;
            if (sourceRootPath == null) {
                newDestinationPath = sourceStart.append(provider
                        .getLabel(nextSource));
            } else {
                int prefixLength = sourcePath
                        .matchingFirstSegments(sourceRootPath);
                IPath relativeSourcePath = sourcePath
                        .removeFirstSegments(prefixLength);
                newDestinationPath = this.destinationPath
                        .append(relativeSourcePath);
            }
            newDestination = workspaceRoot.findMember(newDestinationPath);
            if (newDestination == null)
                continue;
            IFolder folder = getFolder(newDestination);
            if (folder != null) {
                if (policy != POLICY_FORCE_OVERWRITE) {
                    if (this.overwriteState == OVERWRITE_NONE
                            || !queryOverwrite(newDestinationPath)) {
                        noOverwrite.add(folder);
                        continue;