-- Fix issue with setpaths submodules when there's a partial submodules...

function cleanupSharedLibs()

submodules = parseGitSubmodulesFile();

for ii = 1:size(submodules,1)

    submodulepath   = submodules{ii,3};

    if ispathvalid_startup(submodulepath)

        if ispathvalid_startup([submodulepath, '.old/'])

            fprintf('Deleteing folder %s\n', [submodulepath, '.old/']);

            rmdir([submodulepath, '.old/'],'s')

        end

        fprintf('Moving %s  to  %s\n', submodulepath, [submodulepath, '.old']);

        copyfile([submodulepath, '/*'], [submodulepath, '.old/']);

        fprintf('Removing contents of %s\n', submodulepath);

        removeFolderContents(submodulepath);

    end    

    fprintf('\n');

end

 No newline at end of file

    return

end

setNamespace('Homer3');

options = parseOptions(options_str);

if ~options.add

    options.conflcheck = false;

% ----------------------------------------------------

function paths = startupPaths(options_str)

nTries = 2;

h = waitbar(0,'Please wait...downloading shared libraries.');

for iTry = 1:nTries    

    paths = getpathsStartup();

    for ii = 1:length(paths)

        % fprintf('Adding startup path %s\n', paths{ii});

            [cmds, errs, msgs] = downloadSharedLibs(options_str); %#ok<ASGLU>

        end

    end

    try

        setNamespace('Homer3');

        break;

    catch

        cleanupSharedLibs();

    end   

end

close(h)

if ~all(errs==0)

    paths = [];

end

% ----------------------------------------------------

function paths = getpathsStartup()

global startup