This reverts most of commit 3716ba7.

These were not affected by the revert in the previous commit.

In the test suite, a single app is reused for all the converter tests. If the
plugins do not appropriately reset their state at the start of a conversion,
then one test may affect later tests.

The earlier code would skip the creation of a declaration when the
flag excludeNotExported was turned on. This could cause problems
because it is not always possible at the time of the declaration
creation to know whether the declaration will ultimately be
exported. Consider:

const foo =  1;
export { foo }

At the time of processing the first line, it is not known that foo
will be exported.

The new code lets all declarations be created and later, if
excludeNotExported is turned on, it prunes the declarations that
were not exported.

Instead of deciding ahead of time which flags the themes may
need, put all flags in the array and let the themes determine which
flags matter to them.

The Export flag is used to indicate that a symbol is directly under
the effect of an `export` keyword in the TS source or directly subject
to an export declaration.

This flag is different from the Exported flag, which indicates that a
symbol is externally either directly *or* indirectly.

Class members provide a good example of the distinction between the
two flags. They never get the Export flag because they cannot be
individuall exported. However, they have the Exported flag true if
their containing class is exported.

I used ``npm install --package-lock-only`` as specified in the npm doc. Didn't
do any good...

... and rebuild specs for new tests

Also:
- clean up scripts/rebuild_specs.js, making it easier to use for debugging a single test.
- move log message about TS version to the CLI
- Use rimraf instead of rm for Windows compatibility when developing
- Fix bugs with object literals causing a crash, rebuild tests.