ln-010-dev-environment-setup

name	ln-010-dev-environment-setup
description	Installs agents, configures MCP servers, aligns marketplace plugins, creates and audits instructions. Use after setup or when agents/MCP/plugins need alignment.
disable-model-invocation	true
license	MIT

Paths: File paths (references/, ../ln-*) are relative to this skill directory.

Dev Environment Setup

Type: L2 Domain Coordinator Category: 0XX Shared

Runtime-backed coordinator for environment setup. The runtime is the execution SSOT. Worker outputs are standalone summaries, not chat prose.

MANDATORY READ

Load these before execution:

• references/coordinator_runtime_contract.md
• references/environment_setup_runtime_contract.md
• references/environment_worker_runtime_contract.md
• references/coordinator_summary_contract.md
• references/agent_skill_roots_contract.md
• references/environment_state_contract.md
• references/environment_state_schema.json

MCP servers are targets of this workflow, not a prerequisite for starting it. If a server is disconnected or unavailable, continue with file and CLI inspection and report that surface as disconnected or skipped instead of failing the coordinator.

When to Use

• First-time environment setup
• Agent/MCP drift after installs or updates
• Marketplace, plugin, MCP, or Codex execution-default drift across Claude and Codex
• Instruction file audit or repair

Inputs

Parameter	Required	Default	Description
targets	No	both	claude, codex, or both
dry_run	No	false	Plan without mutating
plugins	No	agile-workflow	Pass-through to ln-013. Use an explicit plugin list, or all to request every marketplace plugin. Optional plugins are never installed silently.
auto_install_providers	No	false	Pass-through to ln-013 MCP provider check. When false, provider checks are detection-only.
apply_ide_override	No	false	Pass-through to ln-012 Phase 6b. When true, ln-012 may write claudeCode.initialPermissionMode and claudeCode.allowDangerouslySkipPermissions to Cursor / VSCode user settings after explicit user consent. When false (default), Phase 6b is detection-only and reports drift without mutating IDE settings.

Runtime

Runtime family: environment-setup-runtime

Identifier:

• targets-{normalizedTargets}

Phases:

1. PHASE_0_CONFIG
2. PHASE_1_ASSESS
3. PHASE_1B_PROVIDER_SELECTION
4. PHASE_2_DISPATCH_PLAN
5. PHASE_3_WORKER_EXECUTION
6. PHASE_4_VERIFY
7. PHASE_5_WRITE_ENV_STATE
8. PHASE_6_SELF_CHECK

Terminal phases:

• DONE
• PAUSED

Phase Map

Phase 1: Assess

Collect one environment snapshot:

• agent availability and versions
• MCP registration/connection state
• hook state
• marketplace/plugin alignment state
• Codex skill-root discovery health: active roots, cache roots, duplicate skill names, known_marketplaces.json install-location drift, whether cache is visible under ~/.codex/skills, whether ~/.codex/skills is a whole-root junction to ~/.claude/plugins, and whether approval_policy=never plus sandbox_mode=danger-full-access are already aligned
• graph provider dependency status: for each detected project language, check whether the corresponding graph provider binaries are installed (e.g. basedpyright for Python, csharp-ls for C#). Use mcp__hex-graph__install_graph_providers with mode: "check" if hex-graph MCP is connected
• graph index freshness: whether hex-graph is connected and the project has been indexed in this session (detection-only, no indexing here)
• instruction file state
• disabled flags from .hex-skills/environment_state.json if present
• task management provider availability detection (Linear MCP, gh CLI / Projects v2 readiness, file always available); explicit selection happens in Phase 1b
• research tool detection (Ref → Context7 → websearch)
• git worktree availability
• Claude Code IDE extension state: glob ~/.cursor/extensions/anthropic.claude-code-* and ~/.vscode/extensions/anthropic.claude-code-*. For each found, read claudeCode.initialPermissionMode and claudeCode.allowDangerouslySkipPermissions from the matching IDE user settings.json. Detection-only — no writes here.

Checkpoint payload:

• assess_summary

Phase 1b: Tracker Provider Selection

User selects the task tracker provider (linear, github, file). Selection is persisted in .hex-skills/environment_state.json -> task_management.provider and reused by every task-related skill (ln-200, ln-220, ln-300, ln-401, ln-130, etc.).

MANDATORY READ: Load references/tracker_provider_contract.md before this phase.

Codex exec --full-auto cannot prompt the user mid-run. Selection MUST go through runtime pause + pending_decision + record-decision (NOT AskUserQuestion).

Decision tree:

1. Load Phase 1 availability data and existing task_management from env state.
2. Compute available = filter([linear, github, file], byAvailability):
   • linear available iff Linear MCP server is connected.
   • github available iff gh auth status ok AND repository detected AND (no project_number yet, OR existing project has Status field with all 7 canonical options: Backlog, Todo, In Progress, To Review, To Rework, Done, Canceled).
   • file always available.
3. If task_management.provider is already set AND task_management.status == "active":

node references/scripts/environment-setup-runtime/cli.mjs pause \
  --identifier {identifier} \
  --reason "Confirm tracker provider" \
  --payload '{"kind":"tracker_provider_confirmation","question":"Keep current tracker {provider}?","choices":["keep","switch"],"resume_to_phase":"PHASE_1B_PROVIDER_SELECTION"}'

Resume with set-decision. On keep -> reuse existing provider. On switch -> fall through to step 4.

4. If no current provider OR user chose switch AND available.length > 1:

node references/scripts/environment-setup-runtime/cli.mjs pause \
  --identifier {identifier} \
  --reason "Select tracker provider" \
  --payload '{"kind":"tracker_provider_selection","choices":<available>,"resume_to_phase":"PHASE_1B_PROVIDER_SELECTION"}'

5. If available.length == 1, do NOT pause. Auto-select with selected_by: "single_option" and write the reason (e.g. "Only file mode available because: Linear MCP disconnected, gh CLI not authenticated").
6. Checkpoint Phase 1b:

node references/scripts/environment-setup-runtime/cli.mjs checkpoint \
  --identifier {identifier} \
  --phase PHASE_1B_PROVIDER_SELECTION \
  --payload '{"provider_selection":{"chosen":"<provider>","available":<available>,"reason":"<text>","selected_by":"user|single_option"}}'

Checkpoint payload:

• provider_selection.chosen
• provider_selection.available
• provider_selection.reason
• provider_selection.selected_by

Phase 2: Dispatch Plan

Build selective dispatch plan. Only invoke workers that have work.

Dispatch precedence:

• If marketplace/plugin drift, Codex discovery violation (including whole-root junction), or Codex execution-default drift is present, ln-013-config-syncer becomes mandatory before Codex can be reported as healthy.
• If hex-graph MCP is registered and either (a) graph provider deps are missing for detected project languages, or (b) the project has not been indexed, ln-012-mcp-configurator becomes mandatory even when MCP registration is already complete. ln-012 owns both graph provider dependency installation (PHASE_3) and graph indexing (PHASE_5).

Workers:

• ln-011-agent-installer
• ln-012-mcp-configurator
• ln-013-config-syncer
• ln-014-agent-instructions-manager

Standalone skills packaged in setup-environment but not dispatched by ln-010:

• ln-015-hex-line-uninstaller remains direct-invocation only because it removes existing Claude-side integration surfaces.

Checkpoint payload:

• dispatch_plan

Phase 3: Worker Execution

Invoke only selected workers. Do not re-probe the whole environment between worker calls.

Phase 1 assessment is the shared discovery snapshot. Materialize child manifests from that snapshot and pass them into managed worker runs.

For each selected worker:

• compute deterministic child_run_id
• compute exact child_summary_artifact_path
• checkpoint child_run metadata before delegation
• start the managed environment-worker-runtime child run
• invoke the worker with both runId and summaryArtifactPath
• read the artifact written by the worker
• record the structured worker summary through environment-setup-runtime

Each worker remains standalone-capable, but Phase 3 always uses managed transport.

Expected summary kinds:

• env-agent-install
• env-mcp-config
• env-marketplace-align
• env-instructions

Record summaries with runtime record-worker.

Phase 4: Verify

Run targeted verification against the post-worker state:

• health checks
• hook status
• marketplace/plugin and config alignment status
• Codex skill discovery and execution-default status (including whole-root junction detection)
• instruction file quality
• runtime dependency status (ripgrep, optional language servers)
• graph provider dependency health (basedpyright, scip-python, etc. per project languages)
• graph index status (indexed, skipped, or stale)

Checkpoint payload:

• verification_summary

Phase 5: Write Environment State

Write final durable state to:

• .hex-skills/environment_state.json

Includes all detected sections: agents (with alignment status, marketplace plugins, Codex skill-root health, and Codex execution-default state), task_management, research, claude_md, assessment, hooks, ide_extension (Cursor / VSCode Claude Code extension state from Phase 1 plus any Phase 6b mutations from ln-012).

Rules:

• runtime state is not environment state
• workers never write .hex-skills/environment_state.json
• validate output against shared schema before persisting

Checkpoint payload:

• env_state_written
• final_result

Phase 6: Self-Check

Confirm:

• every required phase checkpoint exists
• dispatched worker summaries were recorded
• final state file was written unless dry_run

Checkpoint payload:

• pass
• final_result

Output Policy

Runtime artifacts:

• .hex-skills/runtime-artifacts/runs/{run_id}/{summary_kind}/{identifier}.json

Durable environment output:

• .hex-skills/environment_state.json

Do not mix these layers.

Worker Invocation (MANDATORY)

Host Skill Invocation: Skill(skill: "...", args: "...") is mandatory delegation.

• Claude: call the Skill tool exactly as shown.
• Codex: if no Skill tool exists, locate the named skill in available skills, read its SKILL.md, treat args as $ARGUMENTS, execute that skill workflow, then return here with its result/artifact.
• Do not inline worker logic or mark the worker complete without executing the target skill.

Phase	Worker	Context
3	ln-011-agent-installer	Install or update CLI agents
3	ln-012-mcp-configurator	Configure MCP servers, hooks, permissions, and IDE extension permission mode (Phase 6b)
3	ln-013-config-syncer	Install/verify Claude and Codex marketplace plugins, align MCP state, and align Codex defaults
3	ln-014-agent-instructions-manager	Create and audit instruction files

node references/scripts/environment-worker-runtime/cli.mjs start --skill {worker} --identifier {childIdentifier} --manifest-file {childManifestPath} --run-id {childRunId} --summary-artifact-path {childSummaryArtifactPath}
node references/scripts/environment-setup-runtime/cli.mjs checkpoint --identifier {identifier} --phase PHASE_3_WORKER_EXECUTION --payload '{"child_run":{"worker":"{worker}","run_id":"{childRunId}","summary_artifact_path":"{childSummaryArtifactPath}"}}'
Skill(skill: "{worker}", args: "{workerArgs} --run-id {childRunId} --summary-artifact-path {childSummaryArtifactPath}")
Read {childSummaryArtifactPath}
node references/scripts/environment-setup-runtime/cli.mjs record-worker --identifier {identifier} --payload '{...environment worker summary...}'

apply_ide_override propagates from ln-010 input to ln-012 only. Default false keeps Phase 6b in detection mode and reports IDE drift as a WARN in the assessment summary; passing true lets ln-012 prompt the user and write Cursor / VSCode settings.

plugins and auto_install_providers propagate from ln-010 input to ln-013 only. Default plugin selection is agile-workflow; optional plugins require an explicit list or all. auto_install_providers=false keeps MCP provider handling detection-only.

TodoWrite format (mandatory)

- Phase 1: Assess (pending)
- Phase 1b: Tracker provider selection (pending)
- Phase 2: Build dispatch plan (pending)
- Phase 3: Start child runtime, checkpoint child metadata, and run selected workers (pending)
- Phase 4: Verify final state (pending)
- Phase 5: Write environment_state.json (pending)
- Phase 6: Self-check (pending)

Critical Rules

• Runtime state is the execution SSOT.
• Do not rely on chat memory for resume or recovery.
• Do not run non-selected workers.
• Do not dispatch ln-015-hex-line-uninstaller from normal setup; it is standalone cleanup.
• Do not repeat full-environment discovery after every worker.
• .hex-skills/environment_state.json is written only in Phase 5.
• dry_run may end with final_result=DRY_RUN_PLAN and skip final state write.

Definition of Done

• Runtime started with identifier-scoped manifest and state
• Assessment snapshot recorded
• Tracker provider explicitly selected by user or single-option-confirmed
• Dispatch plan checkpointed
• Child worker run metadata checkpointed before each delegation
• Worker summaries recorded through machine-readable contract
• Verification summary checkpointed
• .hex-skills/environment_state.json validated and written, or explicit DRY_RUN_PLAN
• Self-check passed

Meta-Analysis

Optional reference: load references/meta_analysis_protocol.md only when the user asks for post-run meta-analysis or protocol-formatted run reflection.

Skill type: domain-coordinator. When requested, run after all phases complete. Output to chat using the protocol format.

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Version: 6.1.0 Last Updated: 2026-04-07