Revise project file I/O to not store list of job ids for each stage

Replaces the code that writes job id lists for each stage in the project.smtk file. The new code reconstructs the job/stage assignments in the project read operation. This keeps/restores the independence between the jobs manifest file and the project file. This change should be backward-compatible with existing project files.

Also includes a couple minor changes to (i) store the acdtool_task for ACDTool jobs and (ii) add a context menu to the NERSC file browser to copy an item's path to the system clipboard.