Port over changes made for paper submission

[yhdengh]

This PR includes changes made for the paper submission that are useful for the master branch.

• Implement functions related to reading directories and testing file existence in Flatware. This allows us to run the CPython without libraries packaged in a virtual filesystem layer.
• Flatware also allows opening a file descriptor for a path. However, it currently does not keep the dirent of an opened path attached at a specific RO table index, and instead re-traverses from the root working directory every time when it needs the dirent. This still needs to be implemented in the future.
• Fix various bugs in scheduler, runtime, and network worker.
• Track total amount of available memory. Jobs that do not have requested memory available are not started until the requested resources are available.
• Add get_shallow_tmp which only loads the top layer of a Tree into memory. select no longer creates a shallow copy of the Tree if it only selects one entry.