- Removed headless_setup call from CLI dispatch entirely. --headless,
--modular, and bare all construct the same SetupPlan with identical
_cfg/zotero_path/agent_type/skip_checks. Only the deprecation notice
differs per entry point.
- Added skip_checks parameter to SetupPlan (forwarded to CLI arg).
- ConfigWriter always writes schema_version '2' unconditionally (never
preserves a v1 value from existing config).
RED commands:
python -m pytest tests/test_setup_plan_v2.py::TestConfigWriterSchemaVersion -v
python -m pytest tests/test_setup_plan_v2.py::TestCliHeadlessViaSetupPlan -v
GREEN commands (same, after fixes): 61/61 passed.
- --headless now delegates to SetupPlan for canonical config, then runs
headless_setup for full deployment; canonical ConfigWriter pass ensures
v2 vault_config format.
- --zotero-data is forwarded through SetupPlan.zotero_path for both
--modular and bare paths.
- Deprecation warnings use print(stderr) instead of filtered
DeprecationWarning so users always see them.
- ConfigWriter.PATH_KEYS extended to converge all seven legacy path keys
(system_dir, resources_dir, literature_dir, control_dir, base_dir,
skill_dir, command_dir) into vault_config, preserving non-path metadata.
- Added CLI-level tests: deprecation on stderr, config canonicalization,
--literature-dir forwarding, --zotero-data plumbing.
ConfigWriter now writes v2 canonical format (nested vault_config with
schema_version). On rerun it merges with existing config rather than
overwriting, making repeated runs idempotent.
load_vault_config reverses the v1 precedence: vault_config block now
wins over legacy top-level path keys, which are treated as a read-only
fallback with a UserWarning. This is the N+1 transition — old v1
configs remain readable with a warning; all writes produce v2 only.
Bare and --headless setup now delegate to the canonical SetupPlan engine
(the --modular path) with a DeprecationWarning.
Closes#75.
