Deprecate reset command

[pjbgf]

The reset and clean commands had an overlap which at times made it harder for users to understand the difference between them. This change deprecates reset in favour of a new flag in the clean command.

Changes

cmd/entire/cli/clean.go — Unified command

• New entire clean defaults to cleaning current HEAD sessions (old reset behavior)
• --all flag for repo-wide orphan cleanup (old clean behavior)
• --session flag for single-session cleanup
• --dry-run flag for preview without action
• --force flag to skip confirmation and active session guard
• --all and --session are mutually exclusive
• Moved activeSessionsOnCurrentHead() here from reset.go
• Added previewCurrentHead() for dry-run support
• Renamed internal functions: runCleanAll, runCleanAllWithItems, runCleanSession

cmd/entire/cli/reset.go — Deprecated wrapper

• Cobra Deprecated field set — auto-prints deprecation warning when used
• Delegates to the same underlying strategy methods
• Keeps --force and --session flags for backward compatibility

cmd/entire/cli/clean_test.go — Comprehensive tests

• Default mode: nothing to clean, force, dry-run, dry-run empty, sessions without shadow branch, multiple sessions, not git repo
• --all mode: no orphans, preview, dry-run, force, sessions branch preserved, not git repo, subdirectory
• runCleanAllWithItems unit tests: partial failure, all failures, no items, mixed types preview
• Flag validation: mutual exclusion of --all and --session

cmd/entire/cli/reset_test.go — Deprecated wrapper tests

• TestResetCmd_IsDeprecated — verifies deprecation field
• Retained core functional tests (nothing to reset, force, not git repo)

Documentation

• README.md — updated command table and troubleshooting section
• docs/architecture/checkpoint-scenarios.md — updated cleanup examples

[Copilot]

Pull request overview

This PR deprecates the entire reset command in favor of a unified entire clean command that supports current-HEAD cleanup by default, plus repo-wide cleanup via --all, with added --session, --dry-run, and --force behaviors.

Changes:

• Updated entire clean to support default current-HEAD cleanup, repo-wide orphan cleanup (--all), single-session cleanup (--session), and dry-run previews.
• Deprecated entire reset via Cobra’s Deprecated field and routed behavior through the same underlying cleanup/reset logic.
• Expanded/adjusted tests and refreshed documentation to reflect the new command semantics.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
cmd/entire/cli/clean.go	Implements the unified clean behaviors (default HEAD cleanup, --all, --session, --dry-run, --force, active-session guard).
cmd/entire/cli/reset.go	Marks reset as deprecated and delegates to the new clean/session logic while keeping compatibility flags.
cmd/entire/cli/clean_test.go	Adds coverage for the new default mode, --all mode, dry-run/force behaviors, and flag validation.
cmd/entire/cli/reset_test.go	Adds a deprecation test and trims/keeps core wrapper behavior tests.
README.md	Updates the command table and troubleshooting/docs to point users to clean (and --all).
docs/architecture/checkpoint-scenarios.md	Updates manual cleanup guidance to use entire clean --all.