feat(cli): restructure CLI around session/checkpoint/agent/auth/doctor

[gtrrz-victor]

https://entire.io/gh/entireio/cli/trails/250

Summary

Reorganizes the flat top-level CLI around noun groups. The command layout now has five domain groups: session, checkpoint, agent, auth, and doctor, plus configure for non-agent settings.

Compatibility policy:

• Same-parent shorthands use real Cobra aliases (sessions, cp, checkpoints).
• Cross-path top-level shortcuts (rewind, resume, attach, explain, trace) stay registered but are hidden and emit a one-line cobra deprecation hint pointing at the canonical group command. They cannot be Cobra aliases because Cobra aliases must share a parent.
• entire configure is the home for non-agent settings (telemetry, git-hook mode, strategy options, summary provider). Agent CRUD lives under entire agent. Bare entire configure prints help and a hint to entire agent.

Closes #1061 once shipped.

Final Command Layout

entire
  ├── activity
  ├── agent
  │   ├── list
  │   ├── add <agent-name>              # flags: --local-dev, --force
  │   └── remove <agent-name>
  ├── auth
  │   ├── login
  │   ├── logout
  │   ├── status
  │   ├── list
  │   └── revoke [id]
  ├── checkpoint                        # aliases: cp, checkpoints
  │   ├── list                          # flags: --session, --no-pager
  │   ├── explain [checkpoint-id|commit-sha]
  │   │   └── flags: --session, --commit, --checkpoint, --short, --full,
  │   │              --raw-transcript, --generate, --force, --search-all,
  │   │              --no-pager
  │   ├── rewind
  │   │   └── flags: --to, --list, --logs-only, --reset
  │   └── search [query]
  ├── clean                             # flags: --all, --session, --force, --dry-run
  ├── configure                         # non-agent settings only
  │   └── flags: --telemetry, --absolute-git-hook-path, --force,
  │              --checkpoint-remote, --skip-push-sessions,
  │              --summarize-provider, --summarize-model,
  │              --local, --project, --local-dev
  ├── disable
  ├── dispatch
  ├── doctor                            # bare runs scan-and-fix
  │   ├── trace
  │   ├── logs
  │   └── bundle
  ├── enable
  ├── login / logout
  ├── session                           # alias: sessions
  │   ├── list
  │   ├── info <session-id> [--json]
  │   ├── stop [session-id]
  │   ├── current
  │   ├── attach <session-id>
  │   └── resume <branch>
  ├── status
  ├── help / version
  ├── hidden top-level shortcuts (functional, emit cobra deprecation hint):
  │   ├── rewind   →  checkpoint rewind
  │   ├── resume   →  session resume
  │   ├── attach   →  session attach
  │   ├── explain  →  checkpoint explain
  │   └── trace    →  doctor trace
  └── hidden:
      ├── search [query]                # → checkpoint search (no hint)
      ├── reset                         # → clean (cobra deprecation message)
      ├── trail (list/create/update)    # experimental
      ├── migrate
      ├── hooks (claudecode/git/...)
      ├── curl-bash-post-install
      └── __send_analytics

What Changed

• Noun-group command structure (wired in cmd/entire/cli/root.go, group roots in <noun>_group.go).
• entire configure keeps non-agent settings (--telemetry, --absolute-git-hook-path, --force, --checkpoint-remote, --skip-push-sessions, --summarize-provider, --summarize-model, --local-dev). Drops --agent, --remove, --yes (those move to entire agent / entire enable).
• Bare entire configure prints help + a hint pointing at entire agent. On a fresh, un-enabled repo it exits early with Run 'entire enable' first. instead of failing inside settings load.
• New updateGlobalSettings helper persists telemetry / hook-mode flags and reinstalls the Entire git hook when --force / --absolute-git-hook-path / --local-dev is set.
• New hideAsAlias(cmd, canonical) helper centralises the Hidden + cobra Deprecated wiring used by the top-level shortcuts.
• checkpoint show is replaced by checkpoint explain (the full explain command).
• Cobra-native aliases (sessions, cp, checkpoints) keep working with no hint; regression test prevents accidental duplicate-root registration.
• Diagnostic commands: session current, doctor logs, doctor bundle.
• Tests: aliascmd_test.go covers hideAsAlias; setup_test.go covers bare-configure help + hint, removed-flag guards, telemetry persistence, conditional hook reinstall, and fresh-repo guard.
• Test / e2e helpers (integration_test/testenv.go, e2e/entire/entire.go, explain/attach/resume tests) now invoke canonical commands so output stays hint-free.
• Updates command-layout documentation in CLAUDE.md and README.md.

Verification

• mise run check (fmt + lint + unit + integration + Vogon/Roger canary E2E)
• go test ./cmd/entire/cli/ -count=1
• go test -tags integration ./cmd/entire/cli/integration_test/ -count=1
• mise run test:e2e:canary (58 vogon + 4 roger-roger, all green)

Notes:

• No paid real-agent E2E suite was run; canaries cover the CLI surface.
• Top-level rewind / resume / attach / explain / trace remain functional; cobra emits a deprecation message on stderr each invocation. Update scripts to the canonical entire <group> <verb> form to silence the hint.

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[Copilot]

Pull request overview

Phase 1 of the CLI noun-group restructure for Entire, reorganizing the command surface around domain nouns (session, checkpoint, agent, doctor) while keeping backwards-compatible top-level entrypoints.

Changes:

• Introduces new noun-group parent commands (session, checkpoint, agent, doctor) and wires them into root.go.
• Adds new subcommands/features: session current, checkpoint diff, doctor logs, doctor bundle, plus an agent CRUD group.
• Adds one-time deprecation warning plumbing for deprecated aliases (e.g. configure → agent) and updates docs/help text.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
cmd/entire/cli/setup.go	Emits one-time deprecation warning when using configure.
cmd/entire/cli/sessions.go	Renames command to session (keeps sessions alias) and registers new children.
cmd/entire/cli/session_current.go	Adds entire session current command.
cmd/entire/cli/root.go	Wires noun groups, keeps top-level compatibility commands, updates Getting Started text.
cmd/entire/cli/doctor_logs.go	Adds entire doctor logs (tail/follow operational log).
cmd/entire/cli/doctor_bundle.go	Adds entire doctor bundle (zip diagnostic bundle).
cmd/entire/cli/doctor.go	Registers trace/logs/bundle as doctor subcommands.
cmd/entire/cli/checkpoint_group.go	Adds entire checkpoint group with list/show/rewind/search/diff.
cmd/entire/cli/checkpoint_diff.go	Implements entire checkpoint diff.
cmd/entire/cli/aliascmd.go	Adds one-time deprecation warning helper.
cmd/entire/cli/agent_group.go	Adds entire agent group with list/add/remove.
CLAUDE.md	Documents the new command layout.

[gtrrz-victor]

Phase 2 added (still draft, additive):

• Hidden configure and reset from --help (both remain functional; configure prints one-time deprecation pointing at entire agent, reset already had Cobra's Deprecated field).
• Refreshed user-facing hints across attach, summary-provider picker, enabled-status, and manage-agents non-interactive error to recommend entire agent ... instead of entire configure --agent ....
• Tests added for Phase 1 surface:
  • aliascmd.warnDeprecatedAliasOnce — prints exactly once per pair
  • computeCheckpointDiff — file delta, token delta, identical, nil tokens
  • readLastNLines + printTail — tail behavior, n=0 copies all
  • writeDoctorBundle — zip contents, omits absent logs/
  • runAgentList — lists registered, marks installed
  • session current — no-session hint, not-a-repo error

Lint + unit + integration + Vogon canary all green. Zero prior-invocation breakage.

[gtrrz-victor]

Follow-up commits on new-command-structure:

• 5da62d0 — Keep entire configure for non-agent settings; hide top-level shortcuts. configure no longer carries --agent / --remove / --yes; bare invocation prints help and points at entire agent. New updateGlobalSettings persists --telemetry / --absolute-git-hook-path / --force / --local-dev and reinstalls the Entire git hook when relevant. New hideAsAlias helper hides rewind / resume / attach / explain / trace at the top level and emits a one-line cobra deprecation hint pointing at the canonical group command. checkpoint show is replaced by checkpoint explain (the full explain command). Test/e2e helpers now invoke canonical commands so output stays hint-free. CLAUDE.md and README.md updated.
• 275ebc5 — entire configure --<flag> on an un-enabled repo now exits early with Run 'entire enable' first. instead of failing inside LoadFromFile. Regression test added.

Verification: mise run check (fmt + lint + unit + integration + Vogon/Roger canary E2E) green on both commits.

[gtrrz-victor]

Addresses Soph's bundle review: redacted by default; --raw to opt out.

• 6ec2dac — entire doctor bundle now scrubs every text entry (.entire/logs/*, settings/*.json, git-*.txt, version.txt) through the redact package before zipping. JSON/JSONL files go through redact.JSONLContent (preserves structure, skips ID fields); everything else through redact.Bytes. The git command outputs were already redacted; this extends the same protection to logs and settings.
• --raw opts out for support workflows that need the full payload. Help text and a stderr mode banner (Bundle written (redacted): <path> / Bundle written (RAW — contains unredacted contents): <path>) make the active mode obvious. Bundle path stays on stdout so $(entire doctor bundle) keeps working.
• New tests cover: log secret redaction, settings credential redaction, --raw passthrough, help-text guard, stderr banner end-to-end.

Verification: mise run lint clean; go test ./cmd/entire/cli/ -count=1 green.