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
}
    /**
     * Sets whether imported file system objects should automatically overwrite
     * existing workbench resources when a conflict occurs.
     *
     * @param value <code>true</code> to automatically overwrite, and 
     *   <code>false</code> otherwise
     */
    public void setOverwriteResources(boolean value) {
        if (value)
            this.overwriteState = OVERWRITE_ALL;
    }
    /**
     * Validates that the given source resources can be copied to the 
     * destination as decided by the VCM provider.
     * 
     * @param existingFiles existing files to validate
     * @return list of rejected files as absolute paths. Object type IPath.
     */
    ArrayList validateEdit(List existingFiles) {
       
        if (existingFiles.size() > 0) {
            IFile[] files = (IFile[]) existingFiles
                    .toArray(new IFile[existingFiles.size()]);
            IWorkspace workspace = ResourcesPlugin.getWorkspace();
            IStatus status = workspace.validateEdit(files, context);
            
            if (status.isMultiStatus())
                return getRejectedFiles(status, files);