feat(physical): first version of physical workflow

[dtulga]

This implements the first version of the physical workflow, as described in #504 This physical workflow (when enabled through the global config or auto-enabled when using QuickStart) auto instantiates and deinstantiates (deletes) the data objects and annotations added or removed to a staged dataset in the current workspace with ADD, DEL, or SYNC. Note that this version only instantiates in the default bare-pairs format and doesn't include options or config values for setting other formats or applying other transformations when auto-instantiating. (These other features, such as options for setting/using other formats and support for transformations will be included in future versions.)

Note that there are a few open questions and other features planned for this workflow (I can add these to this PR if desired, or in a separate change.)

• Adding per-dataset and/or per-workspace setting of whether the physical workflow will be used or not, as well as the preferred format. (The preferred format should also be specifiable in the global config.)
• Adding --format and --apply to add / del / sync to allow specific settings for formats and transformations for the auto-instantiation/deinstantiation
• Add and sync when run on "." currently re-instantiate all data objects and annotations in the current workspace (since these commands seem to imply adding/syncing everything in the current workspace) and I'm unsure if this is desired behavior or if these commands should have a special-case to skip this

[dtulga]

I have updated the code to address the comments, change the formatting, and have tested the modified commands as well. In addition, I added a new --default-physical option to init so that users can turn it on at init if desired - current defaults without specifying options are off for normal init and on for QuickStart. Also feel free to suggest any other output formatting changes if desired!