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
* Creates a new operation that imports specific file system objects.
     * In this usage context, the specified source file system object is used by the
     * operation solely to determine the destination container structure of the file system
     * objects being imported.
     * <p>
     * The <code>source</code> parameter represents the root file system object to 
     * import. Valid types for this parameter are determined by the supplied 
     * <code>IImportStructureProvider</code>. The contents of the source which
     * are to be imported are specified in the <code>filesToImport</code>
     * parameter.
     * </p>
     * <p>
     * The <code>provider</code> parameter allows this operation to deal with the
     * source object in an abstract way. This operation calls methods on the provider
     * and the provider in turn calls specific methods on the source object.
     * </p>
     * <p>
     * The <code>filesToImport</code> parameter specifies what contents of the root
     * file system object are to be imported.
     * </p>
     * <p>
     * The default import behavior is to recreate the complete container structure
     * for the file system objects in their destination. If <code>setCreateContainerStructure</code>
     * is set to <code>false</code>, then the container structure created for each of 
     * the file system objects is relative to the supplied root file system object.
     * </p>
     *
     * @param containerPath the full path of the destination container within the
     *   workspace
     * @param source the root file system object to import from