If a file wasn't required, it won't be in the trackers. This adds those mossing files
968056
def add_missing_covered_codes
      top_level_path = DeepCover.config.paths.detect do |path|
        next unless path.is_a?(String)
        path = File.expand_path(path)
        File.dirname(path) == path
      end
      if top_level_path
        # One of the paths is a root path.
        # Either a mistake, or the user wanted to check everything that gets loaded. Either way,
        # we will probably hang from searching the files to load. (and then loading them, as there
        # can be lots of ruby files) We prefer to warn the user and not do anything.
        suggestion = "#{top_level_path}/**/*.rb"
        warn ["Because the `paths` configured in DeepCover include #{top_level_path.inspect}, which is a root of your fs, ",
              'DeepCover will not attempt to find Ruby files that were not required. Your coverage report will not include ',
              'files that were not instrumented. This is to avoid extremely long wait times. If you actually want this to ',
              "happen, then replace the specified `paths` with #{suggestion.inspect}.",
             ].join
        return
      end

      DeepCover.all_tracked_file_paths.each do |path|
        covered_code(path, tracker_hits: :zeroes)
      end
      nil
    end
736474
public void clearUploadTempData() {
        LOG.debug("Cleaning up temp data...");
        // delete file system zombies
        for (final FileUploadProgress fileUploadProgress : getAllFileUploadProgressValuesFromOverallUploadProcessList()) {
            if (!StringUtils.isBlank(fileUploadProgress.getFilePath())) {
                final boolean deleted = FileUtils.deleteQuietly(new File(fileUploadProgress.getFilePath()));
                if (!deleted) {
                    LOG.warn("TempFile was not deleted: {}", fileUploadProgress.getFilePath());
                }
            }
        }
        clearFileStates();
    }
1177646
def method_missing(m, *args, &block)  
        if @tracker_names.include? m
          @tracker_blocks[m] = block
        else
          super(name, *args, &block)
        end
      end
628585
def download_needed?(task)
      return true if !File.exist?(name)

      if snapshot?
        return false if offline? && File.exist?(name)
        return true if update_snapshot? || old?
      end

      return false
    end
1273139
function selectMissing(missing, manifest, fn) {
  fn(null, manifest.filter(function(file) {
    return file && ~missing.indexOf(file.hash);
  }));
}
1163958
def remove_excludes
      return self if config[:excludes].nil?
      config[:excludes].map { |e| Dir["#{directory}/#{e}"] }.flatten.each do |e|
        FileUtils.remove_entry_secure e
      end
      self
    end
1224957
function( data ){

            var body = data.body
                ,list
                ,minmax
                ,trackedList = this.tracked
                ,tracker
                ,count
                ;

            for ( var i = 0, l = trackedList.length; i < l; ++i ){

                tracker = trackedList[ i ];

                if ( tracker.body === body ){

                    // remove the tracker at this index
                    trackedList.splice(i, 1);

                    for ( var xyz = 0; xyz < maxDof; ++xyz ){

                        count = 0;
                        list = this.intervalLists[ xyz ];

                        for ( var j = 0, m = list.length; j < m; ++j ){

                            minmax = list[ j ];

                            if ( minmax === tracker.interval.min || minmax === tracker.interval.max ){

                                // remove interval from list
                                list.splice(j, 1);
                                j--;
                                l--;

                                if (count > 0){
                                    break;
                                }

                                count++;
                            }
                        }
                    }

                    break;
                }
            }
        }
737433
public synchronized void addDefaultExcludes() {
        int excludesLength = excludes == null ? 0 : excludes.length;
        String[] newExcludes;
        newExcludes = new String[excludesLength + defaultExcludes.size()];
        if (excludesLength > 0) {
            System.arraycopy(excludes, 0, newExcludes, 0, excludesLength);
        }
        String[] defaultExcludesTemp = getDefaultExcludes();
        for (int i = 0; i < defaultExcludesTemp.length; i++) {
            newExcludes[i + excludesLength] =
                defaultExcludesTemp[i].replace('/', File.separatorChar)
                .replace('\\', File.separatorChar);
        }
        excludes = newExcludes;
    }
15516
def filter_exclusions file_paths
      file_paths.reject do |path|
        exclude_file_patterns.any? { |pattern| File.fnmatch("#{pattern}", path) || File.fnmatch("**/#{pattern}", path) }
      end
    end
271799
void deleteNewAndOldFiles() {

        fa.removeElement(fileName + ".data" + ".old");
        fa.removeElement(fileName + ".data" + ".new");
        fa.removeElement(fileName + ".backup" + ".new");
        fa.removeElement(scriptFileName + ".new");
    }
887051
public void spawnTracksFromDetected() {
		// mark detected features with no matches as available
		FastQueue<AssociatedIndex> matches = associate.getMatches();

		int N = detector.getNumberOfFeatures();
		for( int i = 0; i < N; i++ )
			associated[i] = false;

		for( AssociatedIndex i : matches.toList() ) {
			associated[i.dst] = true;
		}

		// spawn new tracks for unassociated detected features
		for( int i = 0; i < N; i++ ) {
			if( associated[i])
				continue;

			Point2D_F64 p = detector.getLocation(i);

			TD d = detectedDesc.get(i);

			CombinedTrack<TD> track;

			if( tracksUnused.size() > 0 ) {
				track = tracksUnused.pop();
			} else {
				track = new CombinedTrack<>();
				track.desc = detector.createDescription();
				track.track = trackerKlt.createNewTrack();
			}

			// create the descriptor for tracking
			trackerKlt.setDescription((float)p.x,(float)p.y,track.track);
			// set track ID and location
			track.featureId = totalTracks++;
			track.desc.setTo(d);
			track.set(p);

			// update list of active tracks
			tracksPureKlt.add(track);
			tracksSpawned.add(track);
		}
	}
1260794
def cleanup(self):
        
        with LogTask('Stop prefix'):
            self.stop()
        with LogTask("Tag prefix as uninitialized"):
            os.unlink(self.paths.prefix_lagofile())
501868
private Boolean isActionNeeded(Collection<File> createdFiles, Collection<File> modifiedFiles) {
        boolean actionNeeded = false;

        for (File createdFile : createdFiles) {
            if (currentlyDeletedFiles.contains(createdFile)) {
                currentlyDeletedFiles.remove(createdFile);
                actionNeeded = true;
            }
        }

        if (modifiedFiles.isEmpty() == false) {
            actionNeeded = true;
        }
        return actionNeeded;
    }
409774
private synchronized void clearCaches() {
        fileListMap.clear();
        includeNonPatterns.clear();
        excludeNonPatterns.clear();
        includePatterns = null;
        excludePatterns = null;
        areNonPatternSetsReady = false;
    }
1292535
function skip() {
    rimraf(file, function() {})
    delete f.versions[v]
    if (f._attachments)
      delete f._attachments[file]
    need.splice(need.indexOf(v), 1)
    maybeDone(null)
  }
1003796
function getNotLoadPackedFiles(page, packedFiles, loadPackeFiles) {
    var existedMap = {};
    loadPackeFiles.forEach(function(item) {
        existedMap[item.id] = true;
    });

    var notExisteds = [];
    packedFiles.forEach(function(item) {
        var pkg = item.pkg;
        var host = item.host;
        if (!existedMap[pkg.id] && (host === page || host == null)) {
            notExisteds.push(pkg);
        }
    });

    return notExisteds;
}
1029836
def addTorrentWithoutMetainfo(announceUrl, infoHash, magnet = nil)
      raise "addTorrentWithoutMetainfo should be called with a Magnet object, not a #{magnet.class}" if magnet && ! magnet.is_a?(MagnetURI)
      trackerclient = TrackerClient.create(announceUrl, infoHash, 0, false)
      addTorrent(trackerclient, infoHash, nil, magnet)
    end