Cylc-flow: Revisit CYLC_DIR use

[kinow]

We had a few hiccups with CYLC_DIR when adding setup.py to the project (#2989). That's due to how setuptools installs python projects, where files may use multiple folders, so there's no more concept of CYLC_DIR after this.

Using Anaconda and virtual environments, it's not necessary to have CYLC_DIR any longer. A few fixes were done for #2989, but there might be still some commands using it (and perhaps working or not).

[hjoliver]

@kinow - I guess the point of this issue is just to check for any remaining use of CYLC_DIR and remove it, after #2989 is merged?

[kinow]

That's right @hjoliver. A just-in-case issue

[hjoliver]

I'm working on getting rid of CYLC_DIR, will post a PR soon. Some details: