Refactor the LinkedFiles/Agent system, and track build_id for output files

app/coffee/Features/Compile/ClsiManager.coffee

app/coffee/Features/LinkedFiles/LinkedFilesController.coffee

app/coffee/Features/LinkedFiles/LinkedFilesErrors.coffee

app/coffee/Features/LinkedFiles/LinkedFilesHandler.coffee

app/coffee/Features/LinkedFiles/ProjectFileAgent.coffee

...coffee/Features/LinkedFiles/ProjectOutputFileAgent.coffee

app/coffee/Features/LinkedFiles/UrlAgent.coffee

app/coffee/infrastructure/FileWriter.coffee

...offee/ide/file-tree/controllers/FileTreeController.coffee

test/acceptance/coffee/LinkedFilesTests.coffee

test/acceptance/coffee/helpers/MockClsiApi.coffee