[stm] [flags] Move document mode flags to the STM.

We move toplevel/STM flags from `Flags` to their proper components;
this ensures that low-level code doesn't depend on them, which was
incorrect and source of many problems wrt the interfaces.

Lower-level components should not be aware whether they are running in
batch or interactive mode, but instead provide a functional interface.

In particular:

== Added flags ==

- `Safe_typing.allow_delayed_constants`
  Allow delayed constants in the kernel.

- `Flags.record_aux_file`
  Output `Proof using` information from the kernel.

- `System.trust_file_cache`
  Assume that the file system won't change during our run.

== Deleted flags ==

- `Flags.compilation_mode`
- `Flags.batch_mode`

Additionally, we modify the STM entry point and `coqtop` to account
for the needed state. Note that testing may be necessary and the
number of combinations possible exceeds what the test-suite / regular
use does.

The next step is to fix the initialization problems [c.f. Bugzilla],
which will require a larger rework of the STM interface.

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