fix: also wrap logging for sub apps

[EspenAlbert]

ask-shell configure_logging now walks the full Typer tree (registered_groups / typer_instance) and applies the same progress and run-log wrapping to subcommands as to top-level commands. tfdo keeps a single root configure_logging(app) in cli.py (no per-subapp calls).

Reviewer notes

• Run log layout change: Nested commands use {root}/{group}/…/{command} (e.g. tfdo/schema/diff) instead of {root}/{command}. Anything that assumed a flat prefix under the root app name should be updated.
• Typer internals: The walk uses registered_commands and registered_groups; if Typer changes these attributes, this needs a follow-up.
• Breaking change: Only for consumers that parse or depend on the old flat run-log path for nested CLIs; API of configure_logging is unchanged.

Risks

• Deep or dynamic trees: Same recursion depth as the Typer graph; unusual plugins with cycles would not be expected but are not guarded.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.68%. Comparing base (1dcc52a) to head (d6185ea).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #11      +/-   ##
==========================================
- Coverage   82.70%   82.68%   -0.03%     
==========================================
  Files          20       20              
  Lines        1833     1842       +9     
==========================================
+ Hits         1516     1523       +7     
- Misses        317      319       +2     

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