Remove ~30 dead CLI subcommands

[osilkin98]

Context

The factory CLI currently exposes ~70 top-level subcommands. After removing dead modes (#1346) and dead infrastructure modules (#1348), ~30 subcommands have no remaining backing implementation.

CLI subcommands to remove

Experiment lifecycle (improve/research-only)

• begin, finalize — experiment lifecycle
• history, diff, explain — experiment analysis (read .factory/results.tsv)

Research/meta-only

• baseline — eval baseline for improve/research score-delta flow
• adversarial-state — GAN-style adversarial loop inspection
• insights, report-update — cross-project reporting
• eval — not invoked by design/create
• leakage-check, validate-research — research-mode ground-truth isolation checks

Backlog/refinement (improve-only)

• backlog-add, backlog-list, backlog-remove — backlog management
• refine-status, refine-begin, refine-complete — refinement loop
• message — CEO messaging

Reporting/analysis

• status, summary, export — reporting/analysis
• research (citation index)
• review — structured PR review for keep/revert loop
• clean-pr — Clean PR Mode (keep module per Akash, but evaluate if CLI verb is needed)

Infrastructure management

• registry-list — cross-project registry listing
• dead-code — zero documentation, unclear purpose
• plugins — generic plugin discovery listing
• runners — runner management (only claude left)
• usage — per-agent token breakdown across runners
• self-update — CLI self-upgrade
• home — trivial, prints install root
• profile — user profile management

Migration/one-time tools

• backfill-citations, backfill-archive — migration tools

Consider keeping as internal (not user-facing)

• log, emit — keep as internal functions, remove CLI verbs
• checkpoint, resume — keep module per Akash, remove CLI verbs if not needed by design/create

Implementation

• Remove subcommand registrations from factory/cli/_main.py handler dispatch table
• Remove parser definitions from factory/cli/_parser_groups.py
• Remove cmd_* functions from factory/cli/ modules where they exist solely for removed commands
• Keep all modules that Akash's PR Dead-code pruning report — comprehensive analysis of ~7,800 removable lines #1302 marks as "actively used" — only remove the CLI verb, not the underlying module

Related

• Depends on Remove dead workflow modes from definitions.py and registry #1346 (dead modes) and Remove dead infrastructure modules (store.py, strategy.py, insights.py, etc.) #1348 (dead modules)
• Related to CLI simplification (CLI simplification: two-tier --help and command consolidation #1351 — two-tier help)
• Dead-code pruning report — comprehensive analysis of ~7,800 removable lines #1301 (dead-code pruning report)

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