Remove SandboxFlags from public API surface

The SandboxFlags expose internal details that are not suitable for
consumption by plugin authors.

Change summary:

  * sandbox/sandbox.py: Remove SandboxFlags as argument in public API
    surfaces, and expose a boolean `root_read_only` argument instead,
    while providing an internal `Sandbox._run_with_flags()` API for
    internal use.

  * __init__.py, sandbox/__init__.py:
    Updated to remove SandboxFlags from public API

  * buildelement.py, scriptelement.py, plugins/elements/autotools.py,
    plugins/elements/compose.py, plugins/elements/manual.py:
    Stop using SandboxFlags, use `root_read_only` parameter instead.

  * element.py: Adapt to API changes, use internal `_run_with_flags()` only
    for special cases such as running shells.

  * sandbox/_sandboxbuildboxrun.py, sandbox/_sandboxdummy.py,
    sandbox/_sandboxreapi.py: Adapt to API changes

Fixes #265
12 files changed