Initialize Project for Claude Code or Codex

File semantics

Read $CLAUDE_PLUGIN_ROOT/skills/init/references/managed-files.md before writing. Record only files and settings entries this run actually installs; unknown ownership is preserved and reviewed. Three classes govern every file this skill writes.

Under Codex, preserve existing hooks/settings throughout this run; the Generated-file overwrite rule below does not apply to hooks.

• Generated — hooks installed by init and .claude/docs/coding-guidelines.md: refresh only unchanged, recorded Optimus files with refresh: "template". Customized files remain refresh: "review" even after approved edits update their recorded hash. Changed, review-only, or unrecorded existing files get that reference's Merge / Keep existing / Replace choice, preserving their content by default; an unrecorded file byte-identical to the current template is adopted silently. Never overwrite unrelated .claude/hooks/* files.
• Customizable — all CLAUDE.md files, testing.md, styling.md, architecture.md, skill-writing-guidelines.md: never silently overwrite. When the file exists, review-and-propose — compare against the template and detected state, apply only user-approved changes, preserve user-added sections.
• settings.json — always merge, never overwrite: preserve permissions and any other custom sections. Do not create it when no hooks are installed and it doesn't already exist.

New files of any class are written directly — no confirmation prompts. Preserve when unsure: content not derivable from the codebase is never discarded, not even to meet size targets. Mark content outdated only when source code directly contradicts it, and confirm with the user before removing user-added items. The same semantics apply to subproject docs in monorepos and to each repo's .claude/ in multi-repo workspaces.

CLAUDE.md authoring rules

Claude Code discovers CLAUDE.md natively; Codex reads it through the AGENTS.md pointer in Step 4c. Spend its context on what reading the repository does not give the model.

• Spend it on gotchas. Invariants a script or CI depends on, a command that must run from a specific directory, a file that looks editable but is generated, a convention the code deliberately breaks in one place, setup that fails in a non-obvious way, why a decision was made. Write fewer real ones rather than padding to a count — an empty Gotchas section is a valid outcome, and better than five lines of restated obviousness.
• Never restate what the filesystem shows. No directory listings, no "the stack is TypeScript" when package.json says so, no per-file roles. One line of identity and stack at the top is the whole allowance.
• Commands do belong here: which of a dozen scripts is the real build/test/lint entry point, with the detected package-manager prefix, is not inferable.
• Target <= 60 lines. The limit is soft: condense template-generated content first; if user-added content still pushes it over, exceed the limit and note the overage in the Step 7 summary.
• Only universally-applicable content — task-specific material distracts the model and degrades instruction-following.
• Progressive disclosure: the Documentation table routes a kind of change to the one doc that governs it, so a typo fix does not load the architecture doc.
• file:line references, not code snippets — snippets go stale.
• Defer mechanical style to the project's configured formatter when present. Preserve existing conventions that tooling does not enforce; Codex and projects declining hooks still need the documented formatter command.
• Monorepo: root CLAUDE.md is an orchestrator — subproject table, workspace-wide commands, workspace-level gotchas only; each subproject's CLAUDE.md carries that package's gotchas (native discovery in Claude Code, explicit nested reads through the Codex pointer). Shared guidelines stay at root .claude/docs/; testing.md/styling.md/architecture.md are scoped per subproject.
• Multi-repo workspace: each repo is fully self-contained (own .claude/); the parent CLAUDE.md is a lightweight local-only map — nothing is shared at root.

Step 1: Detect Project Context

Empty-directory check

A directory is near-empty when it contains at most .git (file or directory), .gitignore, LICENSE, and/or a stub README.md (under 5 lines of non-empty content), with no manifest files at any depth and no source directories (src/, lib/, app/, pkg/, cmd/). If empty or near-empty, use AskUserQuestion — header "Empty Project", question "This directory appears to be empty. Would you like to scaffold a new project?":

• Scaffold new project — "Set up a new project from scratch, then continue with full init setup"
• Continue anyway — "Proceed with init as-is (I'll add code myself later)"

On Scaffold: read and execute $CLAUDE_PLUGIN_ROOT/skills/init/references/new-project-scaffolding.md. If it returns an unsupported-stack signal, apply $CLAUDE_PLUGIN_ROOT/skills/init/references/unsupported-stack-fallback.md (steps 1-4) to find the stack's official scaffolding CLI; if that reaches graceful skip, instead create a minimal project manually (manifest + hello-world entry point + .gitignore) with user approval. After scaffolding, discard all prior detection state and restart Step 1's project detection from scratch.

Project detection (agent-assisted)

Read $CLAUDE_PLUGIN_ROOT/skills/init/agents/project-analyzer.md and launch 1 general-purpose agent with that prompt, prepended with the "Agent Constraints" section of $CLAUDE_PLUGIN_ROOT/references/shared-agent-constraints.md. Assemble the prompt per "Prompt assembly at dispatch time" in $CLAUDE_PLUGIN_ROOT/references/agent-architecture.md — the agent reads the detection references itself via the absolutized paths its prompt carries.

If the agent reports the structure as ambiguous, resolve via AskUserQuestion: ask the user to confirm whether this is a monorepo and identify subproject directories.

Checkpoint

Print the agent's results as a Detection Summary. If a field of its return format came back empty or absent (project name through Gotchas), fill that specific gap yourself — don't re-run the detection the agent just did. An empty Gotchas list is a legitimate answer, not a gap: fill it only if you already know of one this project has. If no test infrastructure was detected, append:

Tests: No test framework, test script, or test directory detected — Step 5b will offer to install one. Strongly recommended: multiple optimus skills depend on test infrastructure.

Then use AskUserQuestion — header "Detection", question "Does the detection summary look correct?":

• Proceed — "Everything looks right — continue with setup"
• Correct — "I need to fix something before continuing"
• Abort — "Cancel init"

On Correct: ask what to change, update the detection results, and re-present the same gate.

Step 1b: Documentation audit (only when the inventory found existing docs)

$CLAUDE_PLUGIN_ROOT/skills/init/agents/documentation-auditor.md defines the audit — its classification levels, its standard of proof, and its Audit Report shape. When the inventory found only a handful of small docs, run it yourself: reading six files and classifying them is a handful of tool calls, and the content stays in context for the Step 2 edits that follow. Delegate to 1 general-purpose agent with that prompt when the doc surface is large enough to be worth isolating, prepended with the same "Agent Constraints" section plus the Detection Results from Step 1 (same prompt-assembly rule). Either way, present the Audit Report to the user.

Standard of proof: only content directly contradicted by source code is Outdated. When a user-added item looks outdated, confirm via AskUserQuestion before discarding — the user may have context the codebase doesn't show.

Use AskUserQuestion — header "Audit", question "How would you like to handle the documentation audit findings?":

• Update all — "Apply all recommended changes"
• Selective — "Pick which findings to apply by number" (then ask for the numbers; unapproved findings are left as-is)
• Fresh start — "Regenerate template content from scratch, but carry forward user-added sections"

Steps 2-6 apply this choice; Step 6b runs independently. Fresh start preservation: extract all User-added content first; after regenerating, re-insert it into the most appropriate sections and present the merged result before writing.

Step 2: Handle Existing Files

Apply the audit choice through the File semantics classes: Accurate → skip the file; Outdated → apply only approved changes, preserve everything else; Missing → create normally; Fresh start → regenerate Customizable files, always carrying User-added content forward. Refresh Generated files only under the ownership rules above. No audit is not permission to replace an existing file.

Relocate when scope changes (e.g., root .claude/docs/testing.md → subproject-scoped in a monorepo): move the content, remove the old file. Only coding-guidelines.md and skill-writing-guidelines.md stay at root. If a root-level CLAUDE.md exists outside .claude/, suggest removing it once .claude/CLAUDE.md is created.

Step 3: Create Directory Structure

mkdir -p .claude/docs .claude/hooks
# Monorepo: also mkdir -p <subproject>/docs per subproject
# Multi-repo workspace: run inside each repo (each gets its own .claude/)

Step 4: Create CLAUDE.md

Fill every template placeholder with real detected values — no [placeholder] text may survive (Step 7 verifies). Each template's HTML comments describe rows init adds conditionally (extra Documentation rows, the skill-authoring route); apply the ones that hold and delete the comment. When updating an existing CLAUDE.md (not Fresh start): edit in place per File semantics — never regenerate from template.

Single project — template $CLAUDE_PLUGIN_ROOT/skills/init/templates/single-project-claude.md:

• Gotchas: from the agent's Gotchas findings and doc-sourced insights. Keep only what survives the template's own bar; drop the section entirely when nothing does.
• Documentation table: the Code row always; one row per non-guideline doc that actually exists — none on a first run, since Steps 5b/6 add entries as they create docs.
• No manifest detected → omit unknown commands and unsupported claims; say which setup information remains unavailable. Never emit a placeholder as a runnable command.

Monorepo — template $CLAUDE_PLUGIN_ROOT/skills/init/templates/monorepo-claude.md:

• Subproject table (path, purpose, stack); root/workspace-wide commands only; workspace-level gotchas only, with package-specific ones pushed down to Step 4b.
• Workspace tool detected → "managed by [tool]"; none → "Monorepo with [N] packages" without naming a tool.
• More than 6 subprojects → group by category in root CLAUDE.md; create or reconcile .claude/docs/architecture.md for the full workspace map and route it from root CLAUDE.md. This root map is an explicit exception to subproject-only architecture placement.
• Root-as-project: also route its root-scoped docs in the Documentation table.

Multi-repo workspace — run the full init flow (Steps 3-7) independently inside each repo, as if init were invoked there (single-project or monorepo template as appropriate; each repo's .claude/ is version-controlled and self-contained). Then create a lightweight workspace-root CLAUDE.md (NOT inside .claude/) from $CLAUDE_PLUGIN_ROOT/skills/init/templates/multi-repo-claude.md — tell the user it is local-only and not version-controlled. If a repo has a nested app root, its CLAUDE.md must note the nested structure and point all commands at the correct subdirectory.

Step 4b — subproject CLAUDE.md files (monorepo only): for each subproject except root-as-project/root-as-member (root CLAUDE.md covers those), use $CLAUDE_PLUGIN_ROOT/skills/init/templates/subproject-claude.md: commands run from its directory, that package's own gotchas, local docs/ routes, parent monorepo named in the opening line.

Step 4c — Codex pointers (root AGENTS.md): When the project shows Codex use — a .codex/ directory or an existing root AGENTS.md — or this session runs under Codex, append the applicable block below or refresh an existing optimus:pointer block, preserving everything outside it. For a single project or monorepo, use the project block at its root. For a multi-repo workspace, use the project block in every child repo and the workspace block at the workspace root. The explicit nested-file routing is necessary because Codex does not automatically load CLAUDE.md files.

Project or child repo:

<!-- optimus:pointer -->
Agent instructions for this project live in `.claude/CLAUDE.md`. Read it first; it routes to the docs under `.claude/docs/`. Before working in a subdirectory, also read the applicable nested `CLAUDE.md` files for package-specific commands, constraints, and doc routes; they are not loaded automatically.
<!-- /optimus:pointer -->

Multi-repo workspace root:

<!-- optimus:pointer -->
Agent instructions for this workspace live in `CLAUDE.md`. Read it first; it maps the child repositories. Before working in a child repo, read its `.claude/CLAUDE.md` and the applicable nested `CLAUDE.md` files.
<!-- /optimus:pointer -->

Step 5: Install Formatter Hooks

Under Codex, skip hook installation and preserve existing hooks/settings byte-for-byte. Document the project's existing formatter/check command for use at task boundaries and its editor/CI integration. This plugin's Claude PostToolUse formatters are not installed in Codex; the documentation and test-infrastructure steps still apply.

Read $CLAUDE_PLUGIN_ROOT/skills/init/references/formatter-setup.md and install the applicable hooks so files are auto-formatted after every Edit/Write (templates in $CLAUDE_PLUGIN_ROOT/skills/init/templates/hooks/; supported: Python, Node.js, Rust, Go, C#/.NET, Java, C/C++, Dart/Flutter — other stacks via $CLAUDE_PLUGIN_ROOT/skills/init/references/unsupported-stack-fallback.md). Hooks are Generated files; settings.json follows its merge semantics. External formatters not already in deps → ask the user before installing.

Step 5b: Test Infrastructure Setup

Read $CLAUDE_PLUGIN_ROOT/skills/init/references/test-infra-provisioning.md.

If test infrastructure was detected in Step 1: run the full procedure — health check (run the suite; fix build/bootstrap failures only with user approval; record assertion failures as {scope, failing_count} for Step 7), coverage-tooling gap check, and provisioning (testing.md, CLAUDE.md refs, README section, .gitignore).

If not detected: use AskUserQuestion — header "Test Infrastructure", question "No test framework was detected. Would you like to install one?":

• Yes (strongly recommended) — "Install test framework and coverage tooling. Multiple optimus skills depend on it: /optimus:tdd is non-functional without tests, and /optimus:deep cannot run safely without a test command."
• No — "Skip test infrastructure setup — some optimus skills will have reduced functionality"

On Yes: follow the reference's installation section (framework recommendation, explicit user approval, install, health check), then the full provisioning. On No: skip all provisioning; Step 7's summary carries the declined-infra note.

Step 6: Create Documentation Files

coding-guidelines.md (Generated) — create in .claude/docs/ from $CLAUDE_PLUGIN_ROOT/skills/init/templates/docs/coding-guidelines.md, replacing [PROJECT NAME], or reconcile the existing file under the ownership rules. Preserve project-specific guidance in place or in an approved, routed document.

Conditional docs (Customizable; testing.md was handled in Step 5b). Fill all placeholders with actual project details:

File	Template	Create when ANY of these hold
styling.md	$CLAUDE_PLUGIN_ROOT/skills/init/templates/docs/styling.md	Manifest lists a UI framework (react, vue, angular, svelte, solid) OR CSS tooling (tailwindcss, styled-components, sass, less, postcss) OR .css/.scss/.less files exist in src/ OR pubspec.yaml has a Flutter SDK dependency
architecture.md	$CLAUDE_PLUGIN_ROOT/skills/init/templates/docs/architecture.md	3+ top-level source directories (excluding config, tests, docs, build output) OR recognized pattern directories (controllers/, services/, repositories/, handlers/, models/) OR skill authoring detected
skill-writing-guidelines.md	$CLAUDE_PLUGIN_ROOT/skills/init/templates/docs/skill-writing-guidelines.md	Skill authoring detected in Step 1 (structural rule in project-analyzer.md task 9)

The architecture template carries two HTML-comment-marked optional sections: keep Skill Architecture only when skill authoring was detected, and keep the code sections (Data Flow, Key Patterns, Dependencies Between Modules) only when the project has code components — delete whichever doesn't apply, and the comments themselves. On re-runs, the Customizable review-and-propose semantics cover section changes when the detected project type has shifted.

Placement: single project — everything in .claude/docs/. Monorepo — styling.md/architecture.md go in each subproject's docs/, applying the detection rules per subproject; retain the root workspace-map exception from Step 4 when needed. skill-writing-guidelines.md is installed once at root when any subproject has a skill-authoring stack; root-as-project's scoped docs go in .claude/docs/; a subproject gets its own coding-guidelines.md only if its conventions differ significantly from root.

Update the Documentation tables: after creating styling.md/architecture.md, add a row to the Documentation table of the CLAUDE.md that scopes it, keyed by the kind of change it governs — "UI, CSS, visual changes", "Module structure or data flow" (testing.md rows were added in Step 5b, keyed "Tests").

Step 6b: Sync Existing Documentation

Skip when the project has no docs of its own (no README.md, CONTRIBUTING.md, ARCHITECTURE.md, or docs/ files). This step runs independently of the Step 1b audit choice (Fresh start governs only .claude/ files) — it operates on project-owned files.

Cross-check README.md (root, and each subproject's in monorepos), CONTRIBUTING.md, ARCHITECTURE.md, and docs/ files that overlap generated topics against source code (manifests, lock files, directory structure). Fix only claims directly contradicted by source — wrong commands or package manager, tech no longer in deps, renamed directories, stale subproject lists, removed dependencies. Surgical, never editorial: leave prose, tone, structure, and imprecise-but-not-wrong descriptions untouched; never add sections or create files; touch nothing outside the project root.

If contradictions found: present a Sync Report (file, current content, proposed fix, source evidence), then use AskUserQuestion — header "Sync", question "How would you like to handle the documentation sync findings?": Apply all / Selective (ask which correction numbers) / Skip sync. Apply only approved changes. If none found, report that and continue.

Step 7: Verify and Report

When Step 5 ran, verify the hooks and settings against their sources before reporting:

• Hooks written this run match their source — each newly copied template hook is byte-identical to its template (diff them), except explicitly approved customizations; custom fallback hooks follow that reference's validation rules. A preexisting hook the user kept is outside this comparison and must remain untouched.
• settings.json survived the merge — every format hook this skill installed has a matching hooks.PostToolUse entry resolving to that installed file. Preserve preexisting entries, including commands outside .claude/hooks/, except exact migrations the user approved. Hooks owned by another skill are out of scope: /optimus:permissions registers restrict-paths.sh under PreToolUse, not PostToolUse. Compare pre/post settings to detect dropped user entries; don't normalize unrelated hooks into this skill's template shape.

Then sweep template-derived content for surviving [placeholder] text and unresolved template HTML comments — retain each file's line-1 identity comment, the optimus:pointer markers in AGENTS.md, and user-authored content. Fix any failure before reporting.

Write the plugin version to .claude/.optimus-version after all checks pass — version string only (e.g., 3.0.0), read from $CLAUDE_PLUGIN_ROOT/.claude-plugin/plugin.json; per repo in multi-repo workspaces. Only init ever writes this file. Then update and verify the ownership record for files/settings installed this run, including this version marker.

Summary — present the final report using this exact format:

### Optimus Init Complete

| Category | Details |
|----------|---------|
| **Project** | [project name] — [tech stack summary] |
| **Structure** | [Single project / Monorepo with N packages / Multi-repo workspace with N repos] |
| **Files created** | [count] files ([list]) |
| **Formatters** | [hooks installed, or "None"] |
| **Test infra** | [Pre-existing: framework / Installed: framework / Not installed] |
| **Doc sync** | [N corrections applied / No contradictions found / Skipped] |

[Monorepo: add subproject breakdown rows. Multi-repo: per-repo results + reminder to commit each repo's .claude/ separately.]

Broken baseline: if the Step 5b health check recorded failing tests, append — baseline broken ([N] failing) to the Test-infra value (per subproject/repo where applicable) and add immediately after the table:

Baseline broken — init does not fix failing tests by design. Ask Claude to triage the failing tests before running skills that need a green baseline.

Conditional warnings after the table:

• Scaffolding created <name>/ → "New project root: the project now lives in <name>/ — start future Claude Code sessions from that directory, or the generated CLAUDE.md and hooks will not load."
• Test framework installed from scratch → "Important: the project has no test files yet, so the test command passes with 0 tests — a false safety net. Run /optimus:unit-test next to write initial tests and establish real coverage."
• Test infrastructure declined → "Note: test infrastructure was not installed — /optimus:tdd will not work, and /optimus:code-review and /optimus:refactor will have reduced functionality. Re-run /optimus:init to install it later."

Close with one line: if the project root has no HOW-TO-RUN.md, recommend running /optimus:how-to-run next; otherwise recommend /optimus:unit-test — in a fresh conversation either way.