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docs(cli): update README and specification to link migration guide and reflect V3-only CLI structure #4380

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opened 2026-04-08 11:29:13 +00:00 by HAL9000 · 0 comments

HAL9000 commented

2026-04-08 11:29:13 +00:00

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Commit Message: docs(cli): update README and specification to link migration guide and reflect V3-only CLI structure
Branch: docs/cli-v3-documentation-updates
Parent Epic: #4182

Background and Context

Epic #4182 identifies that documentation (README, specification) does not reflect the V3-only CLI structure after legacy command removal. Once the migration guide (#4376) and CLI changes (#4181) are complete, the main documentation needs to be updated to reflect the new state.

Expected Behavior

README.md prominently links to the migration guide for users coming from legacy workflow
docs/specification.md CLI Commands section accurately reflects V3-only commands
Any references to legacy commands in documentation are removed or updated
Documentation is internally consistent (no contradictions between files)

Acceptance Criteria

README.md links to docs/Legacy_to_V3_Guide.md
docs/specification.md CLI Commands section reflects V3-only command structure
No references to deprecated legacy commands in main documentation
Documentation is internally consistent
All links in documentation are valid

Supporting Information

Key files: README.md, docs/specification.md (CLI Commands section: lines 199–368)
Related: #4376 (migration guide), #4181 (CLI help output), #4182 (parent epic)
Depends on: #4376 (migration guide must exist first), #4181 (CLI changes must be complete)

Subtasks

Update README.md to add link to migration guide in Getting Started section
Update docs/specification.md CLI Commands section to remove legacy command references
Verify all internal documentation links are valid
Check for any other documentation files referencing legacy commands
Tests (Behave): Add scenario verifying README contains link to migration guide
Run nox (all default sessions), fix any errors
Verify coverage >= 97% via nox -s coverage_report

Definition of Done

This issue is complete when:

All subtasks above are completed and checked off.
All documentation reflects the V3-only CLI structure.
A Git commit is created where the first line of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional details.
The commit is pushed to the remote on the branch matching the Branch in Metadata exactly.
The commit is submitted as a pull request to master, reviewed, and merged before this issue is marked done.
All nox stages pass.
Coverage >= 97%.

Automated by CleverAgents Bot
Supervisor: Product Builder | Agent: epic-planner

## Metadata - **Commit Message**: `docs(cli): update README and specification to link migration guide and reflect V3-only CLI structure` - **Branch**: `docs/cli-v3-documentation-updates` - **Parent Epic**: #4182 ## Background and Context Epic #4182 identifies that documentation (README, specification) does not reflect the V3-only CLI structure after legacy command removal. Once the migration guide (#4376) and CLI changes (#4181) are complete, the main documentation needs to be updated to reflect the new state. ## Expected Behavior - `README.md` prominently links to the migration guide for users coming from legacy workflow - `docs/specification.md` CLI Commands section accurately reflects V3-only commands - Any references to legacy commands in documentation are removed or updated - Documentation is internally consistent (no contradictions between files) ## Acceptance Criteria - [ ] `README.md` links to `docs/Legacy_to_V3_Guide.md` - [ ] `docs/specification.md` CLI Commands section reflects V3-only command structure - [ ] No references to deprecated legacy commands in main documentation - [ ] Documentation is internally consistent - [ ] All links in documentation are valid ## Supporting Information - **Key files**: `README.md`, `docs/specification.md` (CLI Commands section: lines 199–368) - **Related**: #4376 (migration guide), #4181 (CLI help output), #4182 (parent epic) - **Depends on**: #4376 (migration guide must exist first), #4181 (CLI changes must be complete) ## Subtasks - [ ] Update `README.md` to add link to migration guide in Getting Started section - [ ] Update `docs/specification.md` CLI Commands section to remove legacy command references - [ ] Verify all internal documentation links are valid - [ ] Check for any other documentation files referencing legacy commands - [ ] Tests (Behave): Add scenario verifying README contains link to migration guide - [ ] Run `nox` (all default sessions), fix any errors - [ ] Verify coverage >= 97% via `nox -s coverage_report` ## Definition of Done This issue is complete when: - All subtasks above are completed and checked off. - All documentation reflects the V3-only CLI structure. - A Git commit is created where the **first line** of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional details. - The commit is pushed to the remote on the branch matching the **Branch** in Metadata exactly. - The commit is submitted as a **pull request** to `master`, reviewed, and **merged** before this issue is marked done. - All nox stages pass. - Coverage >= 97%. --- **Automated by CleverAgents Bot** Supervisor: Product Builder | Agent: epic-planner

HAL9000 added a new dependency

2026-04-08 11:33:18 +00:00

#4182 Epic: Legacy CLI command removal and full verification of CLI interface and workflows

HAL9000 added a new dependency

2026-04-08 11:33:59 +00:00

#4376 feat(cli): write legacy-to-v3 migration guide and update specification documentation

HAL9000 referenced this issue

2026-04-08 11:34:35 +00:00

Epic: Legacy CLI command removal and full verification of CLI interface and workflows #4182

HAL9000 added this to the v3.5.0 milestone

2026-04-08 17:42:55 +00:00

HAL9000 referenced this issue

2026-04-08 18:43:13 +00:00

[Automated] CleverAgents Build Session - 2026-04-08 #4743

HAL9000 added the

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2026-04-09 01:29:41 +00:00

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auto-arch-4/adr-049-layered-boundary-enforcement

docs/a2a-protocol-autonomy-hardening

auto-arch-9/spec-v3.8.0-milestone-plan

docs/auto-docs-3-reference-index

auto-arch-7/spec-apply-git-worktree

docs/timeline-day104-cycle1-auto-time-4

docs/auto-docs-cycle-1-changelog-updates

auto-arch-6/adr-049-spec-restructuring

docs/auto-docs-1-v340-acms-context-management

docs/auto-docs-1-v320-v330-cli-reference

auto-arch-5/v3.9.0-milestone-plan

test/create-scripts

auto-time-1-day104

timeline/day-104-2026-04-14

docs/auto-time-4-day103-cycle5

auto-time-3-day103-cycle4

auto-docs-5-architecture-overview

spec/three-way-merge-strategy-v3.3.0

spec/checkpoint-system-v3.3.0

auto-docs-4-api-docs-update

auto-docs-1-changelog-expansion

spec/invariant-management-system-v3.2.0

pr-8289

spec/plan-correction-engine-v3.2.0

spec/layered-architecture-boundary-policy

spec/tui-materializer-a2a-integration-v3.7.0

spec/decision-recording-system-v3.2.0

docs/auto-docs-1-milestone-overview

pr-7484

pr-4212

auto-arch-3/v3.8.0-milestone-plan

auto-docs-6/troubleshooting-and-config

auto-time-1-day103-session5

auto-docs-5/contributor-guide-and-readme

docs/plan-tree-ulid-examples

docs/m3-spec-clarify-path-datetime-plugin-contracts

docs/auto-docs-cycle-10-diagnostics-ref

auto-docs-3/user-guide-and-architecture

docs/cycle-7-changelog-update

spec/reconciliation-failure-behavior

auto-docs-2/api-documentation

auto-arch-2/adr-053-repositories-decomposition

auto-docs-1/release-notes-v3.0-v3.1

spec/update-validation-attach-project-delete

spec/architecture-cycle2-impl-clarifications

auto-arch-1/adr-049-052-violations

auto-time-1-day103

docs/auto-docs-cycle-13-updates

docs/timeline-day-102-auto-time

timeline/day-103-2026-04-13

spec/arch-invariant-cli-completeness

spec/update-cycle1-validation-attach-project-delete

docs/add-session-management-showcase

spec/arch-sandbox-path-correction-cycle9

spec/architecture-v380-milestone-plan

docs/auto-docs-cycle-12-updates

docs/cycle-1-validation-gate-fix

docs/2026-04-08-unreleased-changelog

docs/auto-docs-cycle-2-2026-04-10

docs/session-4615-2026-04-08-cycle1

feat/issue-6361-shell-safety-service-tui

spec/architecture-cycle-25-new-features

fix/issue-6345-automation-profile-add-output

docs/timeline-day-102-2026-04-12

docs/cycle-2-git-worktree-acms-hydrator

spec/arch-sandbox-cleanup-discovery

docs/timeline-day96-2026-04-08

docs/auto-docs-cycle-11

spec/fix-sandbox-strategy-protocol-name

spec/arch-acms-tier-hydration

fix/v3.4.0/context-settings-defaults

docs/add-example-repl-and-actor-run

docs/auto-docs-cycle-10-updates

docs/session-4-2026-04-08-updates

docs/showcase-all-examples-consolidated

docs/timeline-day-97

docs/acms-context-hydrator-cycle2

docs/add-example-output-format-flags

spec/arch-failfast-cancel-semantics

timeline/day-101-2026-04-11

docs/timeline-day99-2026-04-09-v2

docs/auto-docs-cycle-2-worktree-acms

spec/architecture-v3.8.0-milestone-plan

docs/api-lsp-acms-reference

improvement/agent-bug-hunt-pool-supervisor-yaml-syntax-fix

spec/project-delete-deleted-at-field

spec/architecture-provider-registry-tui-materializer

spec/document-reconciliation-blocked-error-5942

fix/issue-7482-git-log-injection

spec/devcontainer-auto-discovery-schema

feat/issue-6350-conversation-content-pruning

docs/update-module-guides-2026-04-10

timeline/day-100-2026-04-10-auto-time-cycle1

timeline/day-99-2026-04-09-auto-time-v2

docs/cycle-3-module-guides

timeline/day-99-2026-04-09-auto-time

pr-4226

spec/additional-llm-providers-gemini-groq-cohere-together-ollama-mistral

spec/document-context-tier-hydrator-6175

docs/timeline-day99-2026-04-09

spec/invariant-cli-clarifications

docs/add-example-project-init-and-context-management

spec/reconciliation-blocked-error-documentation

spec/fix-invariant-precedence-reference-5861

spec/fix-plan-correct-accepts-plan-id-5558

spec/fix-validation-attach-synopsis-5328

docs/timeline-day-99-cycle-1

docs/timeline-day-99-cycle-2

fix/actor-context-list-regex-arg

docs/timeline-day-99-cycle-3

spec/arch-security-mode-init

docs/auto-docs-cycle-9-updates

fix-resource-fix-resource-remove-to-check-correct-edge-table

feat/issue-6434-tui-env-var-expansion

fix/issue-6321-plan-prompt-timing-field

fix/issue-6322-resource-add-url-flag

feat/issue-6348-sessions-screen

spec/plan-show-command

temp

feat/harden-label-restrictions-1775753628

spec/invariant-reconciliation-failure-behavior

spec/add-reconciliation-failure-behavior-5942

spec/architecture-corrections-cycle3

spec/checkpoint-trigger-names-and-config-key-fix

spec/fix-ai-provider-interface-5801

spec/azure-api-version-default-update

docs/auto-docs-writer-cycle1-labels

spec/fix-resource-type-yaml-format-5622

spec/add-plan-revert-resume-commands-5574

docs/auto-docs-cycle-1-2026-04-09

spec/plan-correct-plan-id-or-decision-id-5558

spec/fix-subgraph-node-actor-ref-field-5427

issue/5284-master-ci-fix

timeline/day-99-2026-04-09-v2

merge-me

docs/session-3377-initial-docs-update

fix/llm-provider-subpackage-exports

spec/arce-acronym-and-tui-keybinding-fixes

spec/architecture-corrections-cycle2

spec/architecture-corrections-cycle1

docs/cycle-1-updates

spec/tui-clarifications-session-export-persona

docs/session-4940-2026-04-08-cycle1

spec/architecture-milestone-plan-v3.2-v3.7

docs/session-4743-2026-04-08-cycle1

docs/timeline-day-98

fix/plan-lifecycle-service-rollback-method

docs/timeline-day98-2026-04-08-v2

docs/add-example-action-and-plan-management

docs/session-2026-04-06-updates

docs/ca-docs-writer-v3.8.1-2026-04-05

fix/session-tell-stub-missing-panels-and-actor-execution

improvement/agent-arch-guard-clone-failure-handling

improvement/agent-test-infra-health-spam-fix-v2

fix-tdd-invert-non-assertion-exceptions

improvement/agent-arch-guard-clone-failure

bugfix/3472-fix-tdd-inversion-logic

bugfix/989-fix-persistence-json-decode-error

improvement/agent-supervisor-tracking-labels-v2

docs/timeline-day95-v2

docs/timeline-day95-final

docs/update-lsp-api-and-changelog

fix/lsp-resource-handler-module-missing

docs/timeline-day95-final-2026-04-05

fix/a2a-plan-correct-rollback-wiring

docs/add-lsp-api-and-changelog-2026-04-05

fix/tool-registry-validation-type-discriminator

docs/v3.7.0-documentation-update

docs/ca-docs-writer-2026-04-05-cycle2

fix/invariant-set-merge-action-scope

docs/unreleased-feature-docs

fix/concurrency-cost-tracker-record-usage-race-condition

improvement/agent-ca-test-infra-improver-failure-handling

docs/update-changelog-mcp-plan-ci-2026-04-05

improvement/agent-pr-reviewer-milestone-prioritization

docs/timeline-day95-refresh-2026-04-05

improvement/agent-mandatory-labels-tracking-issues

docs/api-domain-providers-changelog-2026-04-05

docs/ca-docs-writer-2026-04-05

docs/timeline-day95-refresh

fix/skill-add-include-validation

docs/timeline-day-95-2026-04-05-update3

docs/timeline-day-95-2026-04-05-update2

docs/ci-incident-runbook-2597

improvement/agent-ca-test-infra-improver-worker-api-mode

docs/shell-safety-api-and-readme-highlights

docs/timeline-day-55-2026-04-04-v2

docs/timeline-day-55-2026-04-04

docs/timeline-day54-update3

improvement/agent-ca-test-infra-improver-fixes

spec/restructure-monolithic-to-split

docs/timeline-day54-update-v2

docs/timeline-day54-update

fix-agents

docs/shell-safety-and-domain-base-model

fix/1452-impl

fix/1473-plan-cancel

fix/1425-test

fix/1426-config

fix/1421-perf

fix/1424-impl

test/int-wf16-devcontainer

feature/m8-tui-persona-export

feature/m7-post-resource-equivalence

test/e2e-m4-acceptance

feature/m6-tantivy-backend

feature/m6-estimation

feature/m6-estimation-report-model

feature/observability-prometheus-audit

feat/server-auth-namespace

feature/m8-session-editing

feature/llm-actor-subplan-wiring

feature/m8-tui-first-run-actor-selection

feature/m8-tui-conversation-block-catalog

feature/m8-tui-settings-screen

feature/m7-e2e-porting

feature/m6-estimation-historical-stats

feature/m8-tui-persona-export-import

feature/m8-tui-sessions-screen

feature/m7-graph-backend

feature/m8-tui-block-context-menu

feature/m8-tui-tool-call-expand

feature/m4-missing-builtin-tools

docs/v3.7.0-release-docs

feature/m8-tui-session-export

test/e2e-wf15-disaster-recovery

test/e2e-wf03-refactoring

test/e2e-m3-acceptance

feature/m8-tui-prompt-history

feature/m8-tui-actor-thought-block-rendering

bugfix/m6-build-hierarchy-child-ids

feature/resource-inheritance-wiring

test/e2e-wf09-session

test/e2e-wf06-doc-generation

test/e2e-wf08-cloud-infra

test/e2e-wf02-test-generation

test/e2e-wf13-custom-profile

test/e2e-wf11-graph-actor

test/e2e-wf01-hello-world

test/int-wf17-explicit-container

test/int-wf12-hierarchical

test/int-wf15-disaster-recovery

test/int-wf13-custom-profile

test/int-wf03-refactoring

test/int-wf11-graph-actor

test/int-wf10-batch

test/int-wf09-session

feature/m3-tdd-issue-consistency-gate

feature/m3-invariant-enforcement-strategize

test/int-wf18-container-clone

test/int-wf01-hello-world

feature/m6-diagnostic-dashboard-health-categories

feature/m6-cli-polish

fix/e2e-db-isolation

feature/m7-post-tui

feature/m9-asgi-endpoint

feature/m7-post-server

tdd/m7-audit-session-race

tdd/m3-skill-add-regression

feature/m9-remote-repos

feature/fs-mount-file-types

tdd/container-resolve-crash

test/e2e-m1-acceptance

test/e2e-m2-acceptance

eugen.thaci-patch-3

eugen.thaci-patch-2

eugen.thaci-patch-1

aditya-fix-latest

feature/m4-secret-masking-llm-context

aditya-fix

refactor/m3-replace-mktemp

refactor/m3-remove-unittest-mock-integration

refactor/m3-remove-robot-mock-imports

refactor/m3-remove-mock-llm-integration

docs/improved-menu-adr

feature/m7-post-auth

feature/m3-fix-resource-bootstrap

feature/post-safety-profile-tests

integration/batch-2026-03-02

feat/slipcover

docs/safety-profile-spec-composition

integrate/freemo-batch-1

feature/m4-error-recovery

feature/m4-security-template

feature/m3-validation-pipeline

develop-aditya-2

feature/m3-diff-review

feature/m3-validation-apply

feature/m6-acp-stubs

feature/m4-correction-flows

feature/m1-plan-execute-runtime

feature/m4-security-exceptions

feature/m4-definition-of-done

feature/m4-correction-model

feature/m1-apply-pipeline

feature/m5-automation-profiles

feature/m2-lsp-stubs

feature/m3-invariants

feature/m1-actor-runtime

feature/docs-v2-restore

feature/m6-perf-scale

feature/m6-validation-edge

feature/m3-session-cli

feature/m1-persistence-tests-robot

feature/m3-config-cli

feature/m1-cli-tests-robot

feature/m5-subplan-tests

feature/m6-review-playbook

feature/aditya-m3-actor-loader

feature/m3-skill-protocol

feature/m4-automation-legacy-cleanup

feature/m3-change-model

feature/m3-skill-git

feature/m3-skill-registry

feature/m4-security-eval

fix/robot-tests

feature/m3-actor-registry

feature/m3-tool-cli

feature/m4-automation-profiles-cli

feature/m2-resource-cli-extensions

feature/m3-actor-loader

feature/m3-tool-domain-robot

feature/m3-skill-domain-robot

feature/m3-skill-cli

feature/m1-resource-db-robot-tests

feature/m3-session-domain-robot

feature/m1-persistence-tests

feature/m1-cli-tests

ten-branches-backup

feature/m3-skill-schema

feature/m3-session-persistence

feature/automation-profiles-and-resource-dag

feature/m1-plan-repo

feature/m1-db-plan-phase-rebaseline

feat/B4-sandbox

feat/B2-cli-wiring

feat/B5-project-persistence

feat/B1-project-data-models

feat/b1-data-models

feat-repo-manager-and-sourcegraph-support

feat/actor-schema

fix/component-isolation-security-fix

feat/ontology-agent

fix/error-handling-security-fix

fix/concurrency-security-fix

fix/serialization-security-fix

fix/server-side-request-forgery-security-fix

fix/file-system-security

fix/template-injection-fix

fix/data-injection-fix

tests/unit-tests

latest/poetry-generator

poetry-generator

config/contract-metadata-extractor

docs/readme-yaml-syntax

config/memory-yaml

fix/double-response

brent-additions

intel_2_demo

auto-working-v6

auto-working-v5

auto-working-v4

auto-before-rewrite-v0

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auto-working-v2

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Blocks

#4182 Epic: Legacy CLI command removal and full verification of CLI interface and workflows

cleveragents/cleveragents-core

Depends on

#4376 feat(cli): write legacy-to-v3 migration guide and update specification documentation

cleveragents/cleveragents-core

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cleveragents/cleveragents-core#4380

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