globally use session-qualified imports; add Lib session

Session-qualified imports will be required for Isabelle2018 and help clarify
the structure of sessions in the build tree.

This commit mainly adds a new set of sessions for lib/, including a Lib
session that includes most theories in lib/ and a few separate sessions for
parts that have dependencies beyond CParser or are separate AFP sessions.
The group "lib" collects all lib/ sessions.

As a consequence, other theories should use lib/ theories by session name,
not by path, which in turns means spec and proof sessions should also refer
to each other by session name, not path, to avoid duplicate theory errors in
theory merges later.

Removes all trailing whitespaces

lib/rule_by_method: add "atomized" attribute

This recovers the original behaviour of the "atomize" attribute,
which converts a Pure rule into a HOL one.

rule-by-method: more robust handling of dummy thms

More struggling due to no proper check for whether or not
a closure is being formed

rule_by_method: better support for method closures

We short-circuit the passed method if it looks like we're making a closure,
instead just emitting a dummy "free" theorem.

Isabelle2016-1: update to new ML API

Update references to renamed ML constants; supply default arguments to
functions with additional parameters; etc.

Isabelle2016-1: work around a find_theorems incompatibility

The new find_theorems tries to inspect rule_prems, which previously
raised an exception within Rule_By_Method. This just makes rule_prems
an empty dynamic fact.

lib/spec/proof/tools: fix word change fallout

resurrected "defs" command for Isabelle2016-RC1

fix lib for isabelle 2016

partial progres in Rule_By_Method

addressed issue with meta-quantifiers

JIRA VER-458

addressed issue with meta-quantifiers

JIRA VER-458

Added Rule_By_Method (@ and # attributes)