all: remove theory import path references

In Isabelle2020, when isabelle jedit is started without a session
context, e.g. `isabelle jedit -l ASpec`, theory imports with path
references cause the isabelle process to hang.

Since sessions now declare directories, Isabelle can find those files
without path reference and we therefore remove all such path references
from import statements. With this, `jedit` and `build` should work with
and without explicit session context as before.

Signed-off-by: Gerwin Klein <gerwin.klein@data61.csiro.au>

ROOT files: file reorg for new ROOT requirements

Isabelle2020 requires each session to declare it own set of directories that
may not overlap with other session's directories. This commit reorganises
files to comply with that requirement.

Signed-off-by: Gerwin Klein <gerwin.klein@data61.csiro.au>