ln-012-mcp-configurator

name	ln-012-mcp-configurator
description	Use when installing MCP packages and configuring Claude-side MCP registration, hooks, permissions, IDE extension mode, and migrations.
license	MIT

Paths: File paths (references/) are relative to this skill directory.

MCP Configurator

Type: L3 Worker Category: 0XX Shared

Invocation is agent-agnostic. Target surfaces are Claude-specific: this skill configures Claude Code MCP settings, hook/style sync, permissions, and Claude Code IDE extension permission mode.

---

MANDATORY READ

MANDATORY READ: Load references/coordinator_summary_contract.md, references/environment_worker_runtime_contract.md, and references/worker_runtime_contract.md

Target MCP availability is not a precondition for this worker. If a server is not connected yet, use config files, package metadata, and CLI state to continue registration and cleanup work; report provider checks or live verification as skipped when they cannot run without MCP.

Input / Output

Direction	Content
Input	OS info, dry_run flag, optional apply_ide_override flag (default false — Phase 6b is detection-only without it), optional runId, optional summaryArtifactPath
Output	Structured summary envelope with payload.status = completed / skipped / error, plus per-server outcomes in changes / detail, plus IDE extension state in payload.ide_extension

If summaryArtifactPath is provided, write the same summary JSON there. If not provided, return the summary inline and remain fully standalone. If runId is not provided, generate a standalone run_id before emitting the summary envelope.

Runtime

Runtime family: environment-worker-runtime

Phase profile:

1. PHASE_0_CONFIG
2. PHASE_1_CHECK_STATUS_AND_VERSION
3. PHASE_2_REGISTER_AND_CONFIGURE
4. PHASE_3_VERIFY_GRAPH_PROVIDER_DEPS
5. PHASE_4_HOOKS_AND_OUTPUT_STYLE
6. PHASE_5_GRAPH_INDEXING
7. PHASE_6_MIGRATE_ALLOWED_TOOLS
8. PHASE_7_PERMISSION_SURFACES
9. PHASE_8_WRITE_SUMMARY
10. PHASE_9_SELF_CHECK

Runtime rules:

• emit summary_kind=env-mcp-config
• standalone runs generate their own run_id and write the default worker-family artifact path
• managed runs require both runId and summaryArtifactPath and must write the summary to the exact provided path
• always write the validated summary artifact before terminal outcome

Output Contract

Always build a structured env-mcp-config summary envelope per:

• references/coordinator_summary_contract.md
• references/environment_worker_runtime_contract.md

Payload fields:

• servers
• permissions
• ide_extension
• hooks_synced
• output_style_synced
• allowed_tools_migrated
• graph_provider_status
• status

---

Server Registry

Two transport types: stdio (local process) and HTTP (cloud endpoint).

Server	Transport	Install	Required	API Key
hex-line	stdio	npx -y @levnikolaevich/hex-line-mcp	Yes	No
hex-ssh	stdio	npx -y @levnikolaevich/hex-ssh-mcp	No	No
hex-graph	stdio	npx -y @levnikolaevich/hex-graph-mcp	No	No
hex-research	stdio	npx -y @levnikolaevich/hex-research-mcp	No	No
context7	HTTP	https://mcp.context7.com/mcp	Yes	Optional
Ref	HTTP	https://api.ref.tools/mcp	Yes	Yes (prompt user)
linear	HTTP	https://mcp.linear.app/mcp	Ask user	No (OAuth)

---

Workflow

Check Status & Version → Register & Configure → Verify Graph Provider Deps → Hooks → Permissions → IDE Extension Mode → Migrate → Report

Phase 1: Check Status & Version

Smart install: check MCP status AND package drift. npx -y caches aggressively — a connected server may still be backed by an older cached package.

Step 1a: Check MCP server status

Run claude mcp list -> parse each hex server:

Server	Status	Action
Registered + Connected	Working	Check version (Step 1b)
Registered + Disconnected	Broken	Re-register (Phase 2)
Not registered	Missing	Register in Phase 2

Step 1b: Version check for connected hex- servers*

For each connected published hex server, run in parallel:

npm view @levnikolaevich/${PKG} version 2>/dev/null

Then compare npm latest against the running local version:

1. npx cache probe: npm config get cache -> scan {cacheRoot}/_npx/**/node_modules/@levnikolaevich/${PKG}/package.json -> pick newest by semver/mtime

Use the npx cache version. If probe returns nothing, report running=unknown and treat the server as refresh-recommended rather than claiming it is current.

Note: published hex packages run via npx -y, NOT global install. Never probe global npm paths.

npm latest	cached local version	Action
Same	Same	SKIP
Newer	Older	Mark "needs update" -> Phase 2 re-registers
Unknown	Any	WARN, proceed

Skip conditions:

Condition	Action
disabled: true	SKIP
dry_run: true	Show planned commands
Connected + cached local version matches npm latest	SKIP, report version

Phase 2: Register & Configure

One pass: use Phase 1 state (do NOT re-run claude mcp list) -> remove unsupported -> register/update -> verify.

1. Reuse Phase 1 state — server map from Step 1a already has registration + connection status
   • Fallback (standalone only): read ~/.claude.json + ~/.claude/settings.json
2. Remove unsupported servers:

Unsupported Server	Action
hashline-edit	Remove if found
pencil	Remove if found
lighthouse	Remove if found
playwright	Remove if found
browsermcp	Remove if found

3. Register missing OR update outdated servers:
   • IF already configured AND connected AND cached local version matches -> SKIP
   • IF connected but outdated -> remove + re-add (forces npx to fetch latest)
   • IF dry_run: true -> show planned command
   • IF linear -> ask user: "Do you use Linear?" -> no -> SKIP

Registration commands (OS-dependent prefix):

OS	Prefix	Why
Windows (bash/MSYS2)	MSYS_NO_PATHCONV=1 claude mcp add ... -- cmd /c npx	MSYS2/Git Bash converts /c -> C:/ in args. MSYS_NO_PATHCONV=1 prevents this
Windows (PowerShell/cmd)	cmd /c npx	No path conversion issue in native shells
macOS / Linux	npx	Direct execution

Server	Command (Windows bash — always prefix with MSYS_NO_PATHCONV=1)
hex-line	MSYS_NO_PATHCONV=1 claude mcp add -s user hex-line -- cmd /c npx -y @levnikolaevich/hex-line-mcp
hex-ssh	MSYS_NO_PATHCONV=1 claude mcp add -s user hex-ssh -- cmd /c npx -y @levnikolaevich/hex-ssh-mcp
hex-graph	MSYS_NO_PATHCONV=1 claude mcp add -s user hex-graph -- cmd /c npx -y @levnikolaevich/hex-graph-mcp
hex-research	MSYS_NO_PATHCONV=1 claude mcp add -s user hex-research -- cmd /c npx -y @levnikolaevich/hex-research-mcp
context7	claude mcp add -s user --transport http context7 https://mcp.context7.com/mcp
Ref	claude mcp add -s user --transport http Ref https://api.ref.tools/mcp
linear	claude mcp add -s user --transport http linear-server https://mcp.linear.app/mcp

4. Verify: claude mcp list -> check all registered show Connected. This is the only second claude mcp list call (post-mutation verify). Retry + report failures.

Windows MSYS2 path validation (MANDATORY on win32): After registration, read ~/.claude.json -> verify each hex server's args[0] is "/c" not "C:/". If corrupted: fix via mcp__hex-line__edit_file (set_line the arg to "/c").

Error handling:

Error	Response
claude CLI not found	FAIL, report "Claude CLI not in PATH"
Server already exists	SKIP, report "already configured"
Connection failed after add	WARN, report detail from claude mcp list
API key missing (Ref)	Prompt user for key, skip if declined

Phase 2b: Verify Graph Provider Dependencies

MANDATORY READ: Load references/hex_graph_provider_matrix.md and references/stack_detection.md.

After registration + connection, verify only the extra system binaries or packages needed for fuller MCP behavior. Assume the project already has its own runtimes and app dependencies. This phase does NOT install project dependencies, framework packages, or runtimes.

Step 1: Identify which servers are connected Reuse Phase 2 verification state. Only check deps for connected hex-* servers.

Step 2: Verify hex-line-mcp dependencies

Dependency	Check	Required	Auto-fix	Fallback
ripgrep	rg --version	Yes	See install table	grep_search fails
git	git --version	No	Inform only	changes tool disabled

Ripgrep install by platform:

Platform	Command
Linux (apt)	sudo apt-get install -y ripgrep
Linux (yum)	sudo yum install -y ripgrep
macOS	brew install ripgrep
Windows (winget)	winget install BurntSushi.ripgrep.MSVC
Windows (scoop)	scoop install ripgrep
Fallback (npm)	npm exec --yes -- @vscode/ripgrep-postinstall

If rg --version fails: ask user whether to auto-install (suggest platform-appropriate command). If user declines, WARN but continue — hex-line will degrade on grep.

Step 2a: EOL-risk advisory for hex-line

Inspect repo and user EOL policy, but do not rewrite it here:

• .gitattributes for eol= / text=auto
• .editorconfig for end_of_line
• git config --get core.autocrlf
• git config --get core.eol
• git config --get core.safecrlf

Report WARN when repo policy and user working-tree policy are likely to churn line endings during normal edits. This is advisory only — do not auto-edit repo policy files in ln-012.

Step 3: Detect current project language(s) for hex-graph

Detect from the current project root only:

1. docs/project/tech_stack.md if present
2. marker files in the project root
3. fallback source-extension scan

Use framework markers only to confirm language:

Framework hint	Language
FastAPI, Django, Flask	Python
ASP.NET Core	C#
Laravel	PHP
React, Next.js, Express, NestJS	JavaScript / TypeScript

If no relevant language is detected for hex-graph, skip the optional provider checks and report SKIP.

Step 4: Verify hex-graph-mcp graph-specific providers and SCIP exporters

Use the MCP tool install_graph_providers from hex-graph-mcp as the source of truth:

• First call it with mode: "check"
• Reuse its instructions_for_agent output as the remediation text
• Only if the user agrees, rerun it with mode: "install"
• Treat the matrix below as reference policy, not as a second implementation source

Detected project language	Tool	Check	Required	Auto-fix	Fallback
JavaScript / TypeScript	None	None	No	None	Embedded TypeScript precise overlay and SCIP export are already available
Python	basedpyright	basedpyright-langserver --version	No	pip install basedpyright	Python precise analysis skipped
Python	scip-python	scip-python index --help	No	Windows: npm install -g github:levnikolaevich/scip-python#fix/windows-path-sep-regex; macOS/Linux: npm install -g @sourcegraph/scip-python	Python export_scip skipped
C#	csharp-ls	csharp-ls --version	No	dotnet tool install -g csharp-ls	C# precise analysis skipped
C#	scip-dotnet	scip-dotnet --help	No	dotnet tool install -g scip-dotnet	C# export_scip skipped
PHP	phpactor	phpactor --version	No	Project-specific PHP install path	PHP precise analysis skipped
PHP	scip-php	scip-php --help or php vendor/bin/scip-php --help	No	composer global config repositories.levnikolaevich-scip-php vcs https://github.com/levnikolaevich/scip-php then composer global require davidrjenni/scip-php:dev-fix/windows-runtime-fixes --prefer-source	PHP export_scip skipped

For hex-graph, think only about graph-specific providers and optional SCIP exporters:

• DO install or recommend basedpyright, csharp-ls, phpactor, scip-python, scip-dotnet, and scip-php when their language is detected
• DO prefer the patched scip-python install on Windows until the upstream Windows fix is released
• DO mention HEX_GRAPH_SCIP_PYTHON_BINARY when a patched Python SCIP binary lives outside the default PATH
• DO prefer the isolated patched scip-php fork for PHP SCIP export when project-local Composer install is blocked or the upstream binary emits an empty artifact
• DO NOT install python, .NET, php, fastapi, django, laravel, nestjs, or any project dependency
• DO NOT install anything for framework overlays alone; Stage 4 framework support is parser/convention-based
• Ask the user before any provider install command

Step 5: Verify hex-ssh-mcp dependencies

No system dependencies (pure JS ssh2). Skip.

Step 6: Report dependency table

Print table with columns: Server | Dependency | Status | Action.

Status	Meaning
OK	Available and functional
INSTALLED	Was missing, auto-installed
WARN	Missing, user declined install
SKIP	Not needed for detected project language(s)
FAIL	Required, cannot install

Error handling:

Error	Response
Required dep missing + user declines	WARN, continue with degraded functionality
Auto-install fails	WARN, show manual install instructions
Optional dep missing	INFO, note in report

For hex-graph, also report the detected language(s) that drove the provider/exporter checks.

Phase 3: Hooks & Output Style [CRITICAL]

Do NOT call setup_hooks. hex-line now auto-syncs hooks and output style on MCP server startup.

After all Phase 2 registrations complete:

1. Trigger one harmless hex-line call to start the server, for example mcp__hex-line__inspect_path({ path: "{project_path}" })
2. Verify the startup sync results below

Hooks (in ~/.claude/settings.json):

1. PreToolUse hook — redirects built-in Read/Edit/Write/Grep/Glob to hex-line equivalents (Glob -> inspect_path(pattern=...))
2. PostToolUse hook — compresses verbose tool output (RTK filter)
3. SessionStart hook — injects MCP Tool Preferences reminder
4. disableAllHooks: After verifying hooks are synced, read ~/.claude/settings.json, set disableAllHooks: false (merge, preserve all other fields), write back. This is appropriate here because the user explicitly invoked setup and wants hooks active. autoSync does NOT manage this flag — it only syncs hook file content and entries.

Output Style: 5. Copies output-style.md to ~/.claude/output-styles/hex-line.md 6. Sets outputStyle: "hex-line" if no style is active (preserves existing style)

Verification: Confirm all of the following after the first hex-line tool call:

• ~/.claude/settings.json contains the 3 hex-line hook entries with current command path
• disableAllHooks: false (set explicitly by this skill, not by autoSync)
• ~/.claude/output-styles/hex-line.md exists and matches package content
• outputStyle: "hex-line" is set only when no other style was already active

Hex-line workflow reminder: the synced output style must teach all of the following:

• carry revision into same-file follow-up edits as base_revision
• run verify before delayed or mixed-tool follow-up edits on the same file
• reuse retry_edit, retry_edits, retry_checksum, and retry_plan directly
• treat line-ending policy as preserved file state, not something edit_file should silently normalize

Note: autosync is idempotent. Any later hex-line startup re-checks installed hook and style content and updates only when they drift.

Phase 4: Graph Indexing

After hex-graph registration + connected status:

1. mcp__hex-graph__index_project({ path: "{project_path}" }) — build initial code knowledge graph
2. If graph-backed reads or edits later look stale, rerun mcp__hex-graph__index_project({ path: "{project_path}" }) — the indexing path is idempotent and refreshes changed files only

Skip if hex-graph not registered or not connected.

Phase 5: Migrate allowed-tools [CRITICAL]

Scan project commands/skills to replace built-in tools with hex-line equivalents in allowed-tools frontmatter.

Tool mapping:

Built-in	Hex equivalent
Read	mcp__hex-line__read_file
Edit	mcp__hex-line__edit_file
Write	mcp__hex-line__write_file
Grep	mcp__hex-line__grep_search
Glob	mcp__hex-line__inspect_path

Steps:

1. Discover .claude/commands/*.md via mcp__hex-line__inspect_path(path=".claude/commands", pattern="*.md", max_entries=0) and .claude/skills/*/SKILL.md via mcp__hex-line__inspect_path(path=".claude/skills", pattern="SKILL.md", max_entries=0)
2. For each file: parse YAML frontmatter, extract allowed-tools
3. For each mapping entry: a. If built-in present AND hex equivalent absent -> add hex equivalent, remove built-in (except Read and Bash) b. If built-in present AND hex equivalent already present -> remove built-in (except Read and Bash) c. Preserve ALL existing mcp__* tools not in the replacement table
4. Write back updated frontmatter (preserve quoting style)

Skip conditions:

Condition	Action
No .claude/ directory	Skip entire phase
File has no allowed-tools	Skip file
All hex equivalents present	Skip file, report "already migrated"
dry_run: true	Show planned changes

Phase 6: Grant Permissions

Instruction files and MCP Tool Preferences content are owned by ln-014-agent-instructions-manager. This skill must not create or rewrite CLAUDE.md or AGENTS.md.

Ensure built-in tools and MCP server prefixes are in ~/.claude/settings.json -> permissions.allow[].

Built-in tools (ensure present):

Tool	Permission entry
Bash	Bash
Read	Read
Write	Write
Edit	Edit
Grep	Grep
WebSearch	WebSearch
WebFetch	WebFetch

MCP servers (per configured):

Server	Permission entry
hex-line	mcp__hex-line
hex-ssh	mcp__hex-ssh
hex-graph	mcp__hex-graph
hex-research	mcp__hex-research
context7	mcp__context7
Ref	mcp__Ref
linear	mcp__linear-server

1. Read ~/.claude/settings.json (create if missing: {"permissions":{"allow":[]}})
2. Consolidate existing entries: For each universal tool (Bash, Read, Write, Edit, Grep, WebSearch, WebFetch, and each mcp__{name}):
   • If specific variants exist (e.g. Bash(gh repo:*), Bash(node ...), WebFetch(domain:docs.github.com)), remove them — the universal entry covers all
   • Pattern: entry.startsWith("Tool(") → remove if universal Tool will be added
3. Add universal entries that are not already present
4. Write back (2-space indent JSON)

Idempotent: existing universal entries skipped. Only specific sub-entries are consolidated into universal ones.

Phase 6b: Verify IDE Extension Permission Mode

The Claude Code IDE extension (Cursor / VSCode) has its own claudeCode.initialPermissionMode setting that overrides permissions.defaultMode from ~/.claude/settings.json when Claude runs through the IDE. Default value is "default" — this silently ignores any project-level bypassPermissions from .claude/settings.local.json. To actually enable bypass when running through the IDE, two extension settings must be set together.

This phase is detection-first. It does NOT modify IDE settings without explicit user consent because permission mode is a security decision and IDE settings are vendor-specific.

Step 1: Detect installed Claude Code IDE extensions

IDE	Extensions directory	User settings path (Windows)	User settings path (macOS)	User settings path (Linux)
Cursor	~/.cursor/extensions/anthropic.claude-code-*	%APPDATA%/Cursor/User/settings.json	~/Library/Application Support/Cursor/User/settings.json	~/.config/Cursor/User/settings.json
VSCode	~/.vscode/extensions/anthropic.claude-code-*	%APPDATA%/Code/User/settings.json	~/Library/Application Support/Code/User/settings.json	~/.config/Code/User/settings.json

For each IDE: glob the extensions directory for anthropic.claude-code-*. If at least one match exists, the extension is installed.

Step 2: Read package.json from extension to enumerate claudeCode.* settings

The relevant keys (verified against extension package.json contributes.configuration.properties):

Setting key	Type	Default	Effect
claudeCode.initialPermissionMode	string enum	"default"	Sets --permission-mode flag at session start. Enum: default, acceptEdits, plan, bypassPermissions
claudeCode.allowDangerouslySkipPermissions	boolean	false	Hard gate — must be true for bypassPermissions to actually engage. Anthropic's explicit guard for IDE contexts

Step 3: Read user settings JSON for each detected IDE and report current state

Detected state	Effective behavior	Reported as
initialPermissionMode absent OR "default", allowDangerouslySkipPermissions absent OR false	Standard prompt-based permissions, project defaultMode IGNORED	default-prompt
initialPermissionMode = "acceptEdits"	File ops auto-approve, Bash still prompts	accept-edits
initialPermissionMode = "plan"	Plan mode forced (no execution)	plan-only
initialPermissionMode = "bypassPermissions", allowDangerouslySkipPermissions = true	Bypass active	bypass-active
initialPermissionMode = "bypassPermissions", allowDangerouslySkipPermissions = false	Misconfigured — user wanted bypass but gate is closed; falls back to default	bypass-blocked

Always include in the report: a one-line explanation of why .claude/settings.local.json defaultMode is silently ignored when running via IDE extension.

Step 4: Cross-check against .claude/settings.json and .claude/settings.local.json defaultMode

If user's project settings declare permissions.defaultMode = "bypassPermissions" but the IDE extension is in default-prompt or bypass-blocked state → emit a WARN in the summary explaining the override:

WARN: Project .claude/settings.local.json declares defaultMode: bypassPermissions, but the Claude Code IDE extension for {IDE} forces --permission-mode {detected} at session start. The project setting is ignored when running through the IDE. To align them, run this skill with apply_ide_override=true and confirm at the prompt, or manually set claudeCode.initialPermissionMode and claudeCode.allowDangerouslySkipPermissions in {settings_path}.

Step 5: Optional remediation (only with explicit user consent)

This phase only writes IDE settings when the caller passes apply_ide_override=true (a separate flag distinct from the main dry_run). Even with the flag, the skill MUST prompt the user with a single confirmation question listing exactly which keys will change in which file.

When applying changes:

1. Backup first: copy settings.json to settings.json.bak.{timestamp} before any write
2. Read → deep-merge → write: preserve every other claudeCode.* key (preferredLocation, useTerminal, respectGitIgnore, etc.) and every non-claudeCode.* key
3. Write only the two keys dictated by the desired mode:
   • For bypassPermissions: set claudeCode.allowDangerouslySkipPermissions: true AND claudeCode.initialPermissionMode: "bypassPermissions"
   • For acceptEdits: set claudeCode.initialPermissionMode: "acceptEdits" (gate not required)
   • For default: remove both keys (or set to false / "default")
4. Instruct full restart: print "IDE restart required (full Quit + reopen, NOT Reload Window) — extension reads settings only at activation"
5. Record in summary: include before/after values, backup path, and the explicit user consent timestamp

Skip conditions:

Condition	Action
No Claude Code IDE extension found	SKIP entire phase, report no-ide
dry_run: true	Detect + report only, no writes (same as default behavior)
apply_ide_override flag absent	Detect + report only, do NOT prompt user
User declines remediation prompt	SKIP write, log decision in summary
Project .claude/settings*.json does not declare defaultMode	INFO: report extension state but no WARN (no conflict to resolve)

Why this phase is detection-first by default:

• IDE settings are per-IDE-vendor and per-user — auto-modifying them across machines is intrusive
• bypassPermissions is a security-sensitive choice; Anthropic explicitly guarded it with allowDangerouslySkipPermissions for IDE contexts (intended for sandboxes without internet)
• Users may legitimately want different modes per IDE (e.g. acceptEdits in Cursor for daily work, bypassPermissions in a separate VSCode profile for sandbox automation)
• Aligns with the no-agent-config-modification rule from the host project memory: detection always, writes only on explicit consent

Phase 7: Report

Status table:

MCP Configuration:
| Server    | Transport | Version | Status        | Permission | Detail                  |
|-----------|-----------|---------|---------------|------------|-------------------------|
| hex-line  | stdio     | 1.5.0   | configured    | granted    | npx package (hex-line-mcp) |
| hex-ssh   | stdio     | 1.2.0   | updated       | granted    | was 1.1.6, now 1.2.0     |
| hex-research | stdio  | 0.1.0   | configured    | granted    | npx package (hex-research-mcp) |
| context7  | HTTP      | —       | configured    | granted    | mcp.context7.com        |
| Ref       | HTTP      | —       | configured    | granted    | api.ref.tools (key set) |
| linear    | HTTP      | —       | skipped       | skipped    | user declined           |

IDE Extension Permission Mode:
| IDE     | Extension Version | initialPermissionMode | allowDangerouslySkipPermissions | Effective State | Conflict with project defaultMode |
|---------|-------------------|-----------------------|---------------------------------|-----------------|-----------------------------------|
| Cursor  | 2.1.92            | bypassPermissions     | true                            | bypass-active   | aligned                           |
| VSCode  | (not installed)   | —                     | —                               | no-ide          | n/a                               |

---

Critical Rules

1. Write only via sanctioned paths. Register servers via claude mcp add. Write to ~/.claude/settings.json ONLY for permissions (permissions.allow[]) or when explicit hook/style verification requires correction after autosync fails
2. Verify after add. Always run claude mcp list after registration to confirm connection
3. Ask before optional servers. Linear requires explicit user consent
4. npx -y for all hex MCP. Never npm i -g — npx provides process isolation and avoids EBUSY on Windows. On Windows, wrap packages with cmd /c npx (see Phase 2 OS prefix table).
5. Remove unsupported servers. Clean up servers no longer in the registry
6. Grant permissions. After registration, add mcp__{server} to user settings
7. Minimize claude mcp list calls. Phase 1 runs it once (discovery). Phase 2 reuses that data. Only Phase 2 Step 4 runs it again (post-mutation verify). Max 2 calls total
8. Always check npm drift. Connected != up to date. Compare npm latest against the newest locally cached npx package version before skipping
9. MSYS2 path safety. On Windows with Git Bash/MSYS2, always prefix claude mcp add with MSYS_NO_PATHCONV=1. After registration, verify args[0] in .claude.json is "/c" not "C:/". Fix inline if corrupted.
10. Verify graph-specific deps after install. After Phase 2 registration, check system binaries for hex-line, graph-specific optional providers, and optional SCIP exporters for detected project languages. Auto-install only with user consent. Never install project runtimes or framework packages here.
11. Report EOL churn risk, do not hide it. If .gitattributes, .editorconfig, or Git config suggest working-tree line-ending rewrites, warn explicitly instead of silently changing repo policy here.
12. Non-destructive config writes. Always read → merge → edit. Never overwrite config files from scratch. Preserve all keys/sections not owned by this skill.
13. IDE extension settings are detection-first. Phase 6b reads claudeCode.* keys from Cursor / VSCode user settings and reports the effective permission mode, but never writes IDE settings without apply_ide_override=true AND an explicit user prompt confirmation. IDE settings are vendor-specific and changing bypassPermissions is a security decision the user must own.

Anti-Patterns

DON'T	DO
Write arbitrary fields to ~/.claude.json	Use claude mcp add for servers; rely on hex-line startup autosync for hooks/style
Skip verification after add	Always check claude mcp list after mutations
Auto-add optional servers	Ask user for Linear and other optional servers
Leave unsupported servers	Remove hashline-edit, pencil, etc.
Calculate token budget	Not this worker's responsibility
Run claude mcp list in every phase	Run once in Phase 1, reuse in Phase 2, verify once after mutations
Assume connected = up to date	Check npm view version vs newest cached npx package version
Assume hooks/style are ready right after registration	Trigger one harmless hex-line tool call, then verify autosync results
Run claude mcp add without MSYS_NO_PATHCONV on Windows bash	Always MSYS_NO_PATHCONV=1 claude mcp add ... or verify+fix args after
Skip provider verification for hex-graph	Detect project language(s) first, then verify only relevant graph-specific providers and SCIP exporters
Auto-install project/framework/runtime packages	Limit this phase to MCP-relevant graph providers and SCIP exporters, and ask user before install
Overwrite entire config file with only known fields	Read existing → deep-merge only owned fields → edit back
Silently flip claudeCode.initialPermissionMode to bypassPermissions because the project asked for it	Detect, WARN about the override, require apply_ide_override=true AND explicit user confirmation before writing IDE settings
Set initialPermissionMode = "bypassPermissions" without also setting allowDangerouslySkipPermissions = true	Both keys are required together — without the gate the mode silently degrades to default
Treat IDE bypassPermissions as a substitute for Codex CLI defaults	Keep Codex execution-default ownership in ln-013-config-syncer
Mutate ~/.codex/config.toml from this worker because it is also permission-related	Route the actual Codex CLI alignment to ln-013-config-syncer
Tell user to use Reload Window after changing IDE settings	Always tell user to fully Quit + reopen — extension reads settings only at activation, not on Reload Window

---

Definition of Done

• MCP packages installed and versions verified against npm registry (Phase 1)
• Missing servers registered and verified connected (Phase 2)
• Outdated servers re-registered with latest version (Phase 2)
• Graph-specific dependencies verified: ripgrep available, detected hex-graph providers and SCIP exporters reported (Phase 2b)
• Hooks auto-synced after first hex-line startup (PreToolUse, PostToolUse, SessionStart, ConfigChange, PermissionDenied) and disableAllHooks: false (Phase 3). MCP config notes: _meta["anthropic/maxResultSizeChars"] up to 500K for large tool results (Claude Code 2.1.91); MCP_CONNECTION_NONBLOCKING env var for -p mode (2.1.89); disableSkillShellExecution setting prevents skill shell execution (2.1.91)
• Output style installed (Phase 3)
• Permissions granted for all configured servers (Phase 6)
• IDE extension permission mode detected for installed Cursor / VSCode and reported with WARN if it overrides project defaultMode (Phase 6b). Writes only with apply_ide_override=true AND user consent.
• Project allowed-tools migrated (Phase 5)
• Status table with version column displayed (Phase 7) including IDE extension permission mode row
• Structured summary returned
• Summary artifact written to the managed or standalone runtime path

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Version: 1.7.0 Last Updated: 2026-04-07