Limit reading/mounting from shared filesystem JobStore

[adamnovak]

This fixes #4673 by adding a --symlinkJobStoreReads option.

If you set --symlinkJobStoreReads=False, we won't create symlinks pointing into a FileJobStore when jobs go to read from it. We will instead make copies or hardlinks (within a filesystem). So if you have a workload that does more I/O on a file mounted into a container than a single full copy would do, you can use this to make a copy happen instead of having everyone mount straight from the shared filesystem.

If you have caching enabled, you can make the cache actually cache a copy per node instead of symlinking all the way through just because it can.

Changelog Entry

To be copied to the draft changelog by merger:

• New --symlinkJobStoreReads=False option lets you force local-node copies (possibly in the cache) even when reading directly from a FileJobStore is possible, potentially reducing shared filesystem IO.

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[DailyDreaming]

Looks good to me, though could something be added to the docs for --symlinkJobStoreReads and when to use it?

Also, particularly: https://github.com/DataBiosphere/toil/blob/7d4d0749e9f5ffcc2a4507e13e940e46400a020d/docs/running/cliOptions.rst