codeindex-cli

A guide to CodeIndex's command-line commands for creating, refreshing, checking, cleaning, and documenting a code index. The index is a searchable map of a project's source code.

In plain words
What is it for?
Use it when explicitly asked to index or reanalyse a repository, check index status, clean stored index data, generate a project wiki, or list indexed repositories.
Why use it?
It clarifies when maintenance commands are appropriate and helps prevent rebuilding or changing an index unnecessarily.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/getklai/klai/codeindex-cli
Any agent
npx skills add GetKlai/klai --skill codeindex-cli
Clone the repo
git clone --depth 1 https://github.com/GetKlai/klai

Made for: Claude Code, Codex.

Per session 77 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,009 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00077 $0.01009
Opus 5 $0.00039 $0.00504
Sonnet 5 $0.00015 $0.00202
Haiku 4.5 $0.00008 $0.00101

Measured 2d ago against content hash 0244ef60ff42, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

codeindex-cli scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/skills/codeindex/codeindex-cli/SKILL.md · 103 lines

How it starts

The opening of the file, as written. The whole thing — 103 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CodeIndex CLI Commands

Use these commands only for explicit index/setup/maintenance requests. For normal agent work, use the MCP tools (query, context, impact) and verify stale results against source files.

Commands

analyze — Build or refresh the index

codeindex analyze

Run from the project root. This parses all source files, builds the knowledge graph, writes it to ~/.codeindex/<ProjectName>/ (global cache — NEVER inside the working copy), and generates CLAUDE.md / AGENTS.md context files in the project root.

Flag Effect
--force Force full re-index even if up to date
--embeddings Enable embedding generation for semantic search (off by default)

When to run: First time in a project or when the user explicitly asks to rebuild the index. Do not run this automatically just because codeindex://repo/{name}/context reports stale data.

For Klai in Conductor, do not run ad hoc analyze/update commands from a feature worktree. That warning can be caused by a worktree overlay or by the registered checkout not being on main. Run scripts/codeindex-health.sh first; only if it reports the shared base index is stale, run scripts/codeindex-health.sh --repair.

update — Refresh an existing index

codeindex update

Use this only when the user explicitly asks to refresh a stale index. For Klai Conductor worktrees, prefer scripts/codeindex-health.sh --repair for the shared main index.

status — Check index freshness

codeindex status

Shows whether the current repo has a CodeIndex index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.

clean — Delete the index

codeindex clean

Deletes the repo's entry under ~/.codeindex/<ProjectName>/ and unregisters it from the global registry. Use before re-indexing if the index is corrupt or after removing CodeIndex from a project. Never deletes anything inside the working copy.

Read the full file on GitHub · 103 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2d ago First seen · 103 lines · 77 tokens per session scan A 0244ef60ff42

Subscribe to this mod's changes

codeindex-cli is a skill published in the GitHub repository GetKlai/klai (11 stars, last pushed 2d ago), licensed MIT. It adds 77 tokens to every session and 1,009 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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