Polishing CLI

[Tiendil]

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[Copilot]

Pull request overview

This PR polishes the Donna CLI by flattening its command structure (removing the workspaces, sessions, and artifacts command groups in favor of top-level commands like init, start, run, list, etc.) and refactors the supporting domain types. It introduces a typed path system (donna/domain/paths.py), splits artifact/section identifiers into helper-driven NewTypes, replaces time-based caching with file-fingerprint-based caching, and accepts root-anchored, relative, or absolute project paths in artifact arguments.

Changes:

• Flatten CLI subcommands and rename action-request-completed to complete-action-request; entry point now uses donna.cli.application:main which registers commands lazily.
• Introduce donna/domain/paths.py typed paths and a new donna/workspaces/paths.py resolver; rewrite artifact_ids around NewType plus helper functions (artifact_section_id, split_artifact_section_id, etc.) and let artifact CLI args accept relative/absolute paths.
• Replace the time-based TimedCache with a FileFingerprint-based cache for artifacts/state, drop the cache_lifetime config option, and add SessionStateChangedExternally error; initialization writes a TOML fixture and no longer eagerly creates the session dir.

Reviewed changes

Copilot reviewed 46 out of 46 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
README.md	Update CLI examples to flattened command names and explain lazy session dir.
pyproject.toml	Point entry point at donna.cli.application:main.
donna/cli/main.py	Delegate to main() instead of importing commands here.
donna/cli/application.py	Add main() that registers commands and runs app.
donna/cli/commands/{workspaces,sessions,artifacts}.py	Drop sub-Typers and register commands directly on app; parse path arguments through new helpers.
donna/cli/types.py	Replace ID parsers with raw-string parsers and parse_artifact_*_argument resolution helpers.
donna/cli/{entities,utils}.py	Use new UntrustedPath/PathInput types.
donna/domain/paths.py	New NewType-based path taxonomy.
donna/domain/artifact_ids.py	Rewrite IDs as NewType plus validation/split/build helpers.
donna/domain/types.py	Remove Milliseconds.
donna/workspaces/paths.py	New module for resolving and normalizing project paths.
donna/workspaces/initialization.py	Write fixture-based config; remove eager session-dir creation.
donna/workspaces/fixtures/base_config.toml	New default config fixture.
donna/workspaces/{config,errors,artifacts,sessions}.py	Switch to new typed paths and helper APIs; add fingerprint-based artifact API.
donna/workspaces/files.py	New FileFingerprint value object.
donna/context/{artifacts,state,primitives}.py	Replace timed cache with fingerprint cache; add external-change detection.
donna/context/entity_cache.py	Removed.
donna/machine/{tasks,state,sessions,errors}.py	Use split_artifact_section_id/artifact_section_id; add SessionStateChangedExternally.
donna/primitives/{artifacts,directives,sections}/*.py	Adopt new artifact-section helpers.
donna/core/utils.py	Return ProjectRootPath from discovery helpers.
donna/skills/fixtures/*.md	Update agent skill docs to flattened CLI.
donna.toml	Drop cache_lifetime.
.agents/donna/, .agents/skills/	Remove obsolete agent docs and skills.

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