diffnames setpath utility, getpaths no longer removes atlasviewer folders from path

if options.conflcheck

    % Get all workspace paths that have similar functions sets with current applications

    appmainfunc = {'AtlasViewerGUI.m','Homer2_UI.m','Homer3.m','brainScape.m','AcqDataClass.m'};

    appmainfunc = {'Homer2_UI.m','Homer3.m','brainScape.m'};

    kk=1;

    wsidx = [];

%           {'mvpathconfl','rmpathconfl'}  (default: mvpathconfl) 'conflcheck' option must be selected

%                                                                  for this this option not to be ignored

%           {'quiet','verbose'}            (default: quiet)

%           {'nodiffnames','diffnames'}    (default: nodiffnames) Diffs files that share a name with a file already on the path

%

%

% EXAMPLES:

%

%     end

% end

% Add or remove paths for this application

rootpath = pwd;

rootpath(rootpath=='\')='/';

paths_str = '';

dnum = 0;

diffqueue = {};  % Files to be diff'd

for ii=1:length(paths)

    paths{ii} = [rootpath, paths{ii}];

    if options.diffnames

        % See if any of the imported functions already exist

        files = dir(fullfile(paths{ii},'*.m'));

        for f = 1:length(files)

            % When exists returns 2 but excluding the working dir

            if ( (exist(files(f).name(1:end-2),'file') == 2) & (~isequal(files(f).folder,pwd())))

                if options.verbose

                    fprintf("This file shadows one already on the path: %s\n",[files(f).folder '\' files(f).name(1:end-2)]);

                    fprintf("Here is the original: %s\n", which(files(f).name(1:end-2)));

                end

                if (strcmp( fileread([files(f).folder '\' files(f).name]), fileread(which(files(f).name(1:end-2))) ))

                    if options.verbose

                        fprintf("The files are the same.\n");

                    end

                else

                    if options.verbose

                        fprintf("The files have some differences.\n")

                    end

                    dnum = dnum + 1;

                    diffqueue{end+1} = {[files(f).folder '\' files(f).name], which(files(f).name(1:end-2))};

                end

            end

        end

    end

    if options.verbose

        if options.add

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

    end

    paths_str = [paths_str, delimiter, paths{ii}];

end

% If there are different files with same name

if dnum > 0  % True only if options.diffpaths is

    fprintf('There are %i files that shadow different files already on the path.\n', dnum);

    diffchoice = input(sprintf('Would you like to diff them now? y/n '),'s');

    if (size(diffchoice,2) > 0) & ((diffchoice == 'y') | (diffchoice == 'yes'))

        for i = 1:size(diffqueue,2)

            % Use visual diff tool

            visdiff(diffqueue{i}{1}, diffqueue{i}{2});

        end

    end

end

% Add current workspace at the top of the stack of conflicting workspaces

wspaths = [pwd; wspaths];

paths_excl_str = [paths_str, paths_excl_str];

% Either add all conflicting workspaces to the search path or remove the

% current one, depending on user selection

if options.add

end

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

function idx = findExePaths(paths)