chore: remove typer[all] extra, add shellingham explicitly

[pavsoss]

Closes #597

This PR addresses the harmless but annoying installation warning caused by the deprecated [all] extra in typer.

• Updated pyproject.toml: Replaced "typer[all]>=0.12.0" with "typer>=0.12.0".
• Preserved Dependencies: Explicitly added "shellingham>=1.5.0" to ensure CLI completions continue working. (rich was already explicitly pinned in the dependencies).

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🧪 PR Test Results

Check	Result
Tests (pytest tests/)	✅ success
Lint (ruff check .)	❌ failure
Coverage (agentwatch)	74.19%

_{Python 3.12 · commit 7dc0db4}