Clean up remaining ruff findings ignored in pyproject.toml

Follow-up to the Build CI fix (pin ruff + scope its rule set): 39 findings needed a deliberate code review rather than a mechanical fix, so they're ignored in pyproject.toml for now:

• LOG015 (20x) / LOG014 (1x) — calls on the root logger; needs per-module loggers introduced deliberately across app.py, rag_system.py, get_knowledge_base.py, get_samples_examples.py.
• BLE001 (6x) — blind except Exception; some of these look intentional (top-level request/error handling), needs a per-call decision.
• RUF012 (5x) — mutable class-attribute defaults, mostly in test mock classes (test_intercom.py).
• PLW1510 (2x) — subprocess.run without an explicit check= argument.
• DTZ011 (1x) — datetime.date.today(), needs a timezone decision.
• SIM102, SIM103, PIE810, EXE001 (1x each) — small mechanical cleanups, lowest risk of the bunch.

None of these are urgent; they're just deferred out of the CI-unblocking PR to keep that change safe and reviewable.

Start in pyproject.toml, then review the listed findings in app.py, rag_system.py, get_knowledge_base.py, get_samples_examples.py, and test_intercom.py. Check each ignored rule, including the subprocess and date cases, and make the per-call decisions described in the issue. Done means the remaining findings are addressed deliberately and the temporary ignores can be removed without breaking CI.