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
monitor.subTask(provider.getFullPath(folderObject));
        IWorkspace workspace = destinationContainer.getWorkspace();
        IPath containerPath = containerResource.getFullPath();
        IPath resourcePath = containerPath.append(provider
                .getLabel(folderObject));
        
        
        if (resourcePath.equals(containerPath))
            return policy;
        if (workspace.getRoot().exists(resourcePath)) {
            if (rejectedFiles.contains(resourcePath))
                return POLICY_SKIP_CHILDREN;
            return POLICY_FORCE_OVERWRITE;
        }
        try {
            workspace.getRoot().getFolder(resourcePath).create(false, true,
                    null);
        } catch (CoreException e) {
            errorTable.add(e.getStatus());
        }
        return policy;
    }
    /**
     * Imports the specified file system object recursively into the workspace.
     * If the import fails, adds a status object to the list to be returned by
     * <code>getStatus</code>.
     *
     * @param fileSystemObject the file system object to be imported
     * @param policy determines how the file system object and children are imported
     * @exception OperationCanceledException if canceled