collectProjectFiles(projectDir, ignorePatterns)

function [filelist] = collectProjectFiles(projectDir, ignorePatterns)
    %COLLECTPROJECTFILES create a filelist of a project ready for packaging
    %
    %Usage: filelist = collectProjectFiles(projectDir, ignorePatterns);
    %
    %filelist:          list of files to be included in the package
    %projectDir:        the root directory of the project
    %ignorePatterns:    files and folders to ignore
    
    %default value
    filelist = [];
    
    %do some basic checks
    if exist(projectDir, 'dir') ~= 7
        %folder does not exist
        filelist = [];
        return;
    end
    if nargin == 1
        ignorePatterns.files = {'^\.', '~$'};
        ignorePatterns.dirs  = {'^\.'};
    end
    
    %collect all the files and folders in the projectDir
    projectContent = dir(projectDir);
    
    %get the relevant fields for processing
    contentName = {projectContent.name};
    dirFilter   = [projectContent.isdir];
    
    %remove the first 2 items ('.' and '..')
    contentName(1:2) = [];
    dirFilter(1:2)   = [];
    
    %remove unwanted folders
    rmUnwantedDirs = cellfun(@(c) regexpi(c, ignorePatterns.dirs, 'once'), contentName, 'UniformOutput', false);
    rmUnwantedDirs = cellfun(@(c) cellfun(@any, c), rmUnwantedDirs, 'UniformOutput', false);
    rmUnwantedDirs = cellfun(@any, rmUnwantedDirs);
    unwantedFilter = all([dirFilter; rmUnwantedDirs], 1);
    
    %remove the undesired folders from the lists
    contentName(unwantedFilter) = [];
    dirFilter(unwantedFilter)   = [];
    
    %add the files in the projectDir
    rootFiles = contentName(~dirFilter);
    
    if isempty(rootFiles)
        %no root files present
        
    else
        %remove unwanted files
        rmUnwantedFiles = cellfun(@(c) regexpi(c, ignorePatterns.files, 'once'), rootFiles, 'UniformOutput', false);
        rmUnwantedFiles = cellfun(@(c) cellfun(@any, c), rmUnwantedFiles, 'UniformOutput', false);
        rmUnwantedFiles = cellfun(@any, rmUnwantedFiles);
        rootFiles(rmUnwantedFiles) = [];
        
        %create full path names
        filelist = cellfun(@(c) fullfile(projectDir, c), rootFiles, 'UniformOutput', false);
    end
    
    if sum(dirFilter) > 0
        %there are subfolders for packaging, get their names
        subdirs = contentName(dirFilter);
        
        %check the subfolders in a recursive manner
        numSubDirs  = numel(subdirs);
        for sd = 1:numSubDirs
            subdir = subdirs{sd};
            subFilelist = collectProjectFiles(fullfile(projectDir,subdir), ignorePatterns);
            if isempty(filelist)
                filelist = subFilelist;
            else
                filelist = [filelist, subFilelist];
            end
        end
    end
end