uncoded 2.1.1

Symbol index with associated code reading tools for AI coding agent navigation

uncoded

AI coding agents navigate codebases poorly. They grep for guessed keywords, skim the first few lines of files, and fill gaps from pretraining rather than reading the actual code. The result is plausible-looking output built on a hallucinated understanding of the code.

uncoded builds a static navigation index for the codebase. Agents load it at the start of a task and navigate directly to what they need, without guessing or grepping.

It also ships uncoded body to read symbol bodies and uncoded refs to find every reference to a symbol. References cover callers, dead-symbol checks, and the full set of sites to update before a rename.

What it generates

Running uncoded sync produces:

.uncoded/namespace.yaml: a hierarchical YAML file listing every symbol: directories, files, classes (with attributes and methods), functions. Covers all configured source roots. An agent can load this at the start of a task and immediately know the full vocabulary of the codebase.

.uncoded/stubs/: one .pyi stub per source file, with imports, full signatures (parameter names, types, return types), module constants, and class attributes.

.uncoded/docs.yaml: a heading outline of configured Markdown files. Each file nests its #-prefixed headings as keys. Leaf headings map to null. Agents load this to orient to the documentation. They then navigate to a heading with Read or grep. uncoded generates it only when doc-roots is configured. It is an outline only. uncoded body, uncoded refs, and stubs do not apply to Markdown.

Skills, written to both .claude/skills/ and .agents/skills/:

• uncoded-code-navigation: the code dispatch rule: load namespace.yaml first, read .pyi stubs before source, use uncoded body and uncoded refs for symbol operations. Generated when source-roots is configured.
• uncoded-doc-navigation: the docs navigation rule: load docs.yaml at session start, then use Read or grep to reach a heading. Generated when doc-roots is configured.
• uncoded-coherence-review: a structured diagnostic sweep for naming drift and incoherence (see Coherence review). Generated when source-roots is configured.

Add these lines to your AGENTS.md or CLAUDE.md to load the navigation skills every session. Skills are on-demand by default. Tying the load to an action agents are about to take prompts them to act on it:

## Before you start

- Load the `uncoded-code-navigation` skill before searching, reading or editing any code.
- Load the `uncoded-doc-navigation` skill before searching, reading or editing any docs.

Install uv

uncoded runs via uv. Install uv if you don't already have it. No separate uncoded install is needed. uvx runs it from PyPI on demand.

Configure

Add a [tool.uncoded] section to your pyproject.toml:

[tool.uncoded]
source-roots = ["src", "tests"]
doc-roots = ["docs", "README.md"]  # dirs walked for *.md, or individual .md files

source-roots and doc-roots are each optional. At least one must be set. source-roots drives the code index (namespace.yaml + stubs). doc-roots drives the doc index (docs.yaml). Entries in doc-roots can be directories (all *.md files walked recursively) or individual .md files.

Non-Python repos can use .uncoded.toml in the project root instead, with the same keys at the top level. No [tool.uncoded] wrapper is needed:

doc-roots = ["docs"]

pyproject.toml takes precedence over a sibling .uncoded.toml only when it carries a [tool.uncoded] section. If both files configure uncoded in the same directory, uncoded reports a configuration error. Configure in one file only.

Across directories, the nearer file wins. uncoded never reads either file from inside the .uncoded/ directory.

Use

uvx uncoded sync

Run uvx uncoded sync from the repo root. It reads pyproject.toml (or .uncoded.toml) to find your configured roots and builds the index and skill files.

Commit the generated .uncoded/ directory so agents working in the repo always have a current index.

Keep it current with pre-commit

Add uncoded sync as a pre-commit hook so the index stays in sync automatically:

- repo: local
  hooks:
    - id: uncoded
      name: uncoded
      entry: uvx uncoded sync
      language: system
      pass_filenames: false

Like ruff format: if uncoded sync modifies any files, the commit fails and you stage the updated index before committing again.

You can also set up your CI to run pre-commit run --all-files to verify the index is up to date.

Verify the index is fresh

Use the check subcommand for CI or scripted checks that must not modify the working tree:

uvx uncoded check

It runs the same pipeline but writes nothing. It exits 0 if every generated file is byte-identical to what a rebuild would produce. It exits 1 otherwise, printing which files would change. A stale index is a silent failure mode. Agents read misleading names and signatures. Gate on this in CI even alongside a pre-commit hook.

Retrieve a symbol body

Use the body subcommand when you need a symbol's implementation, not just its signature from the stub:

uvx uncoded body <name_path> --in <relative_path>

name_path is a slash-separated path: one segment (fn) for a top-level symbol, two for a class member (Class/method). --in is the source file's path (relative to cwd). The command prints the source text of the symbol to stdout, byte-identical to what's on disk. No reformatting, no ast.unparse normalisation.

For example, to retrieve the body of resolve_body from src/uncoded/body.py:

uvx uncoded body resolve_body --in src/uncoded/body.py

Find references to a symbol

Use the refs subcommand for impact analysis. Run it before a rename, signature change, or delete. Run it also to confirm a symbol is dead before removing it:

uvx uncoded refs <name_path> --in <relative_path>

name_path follows the same convention as body: one segment for a top-level symbol, two for a class member (Class/method).

Output is one reference per line as <rel_path>:<line>:<col>. Line and column are 1-indexed. Results are sorted by path, then line, then column. It exits 0 on success. Empty output means no references.

For example, to find all callers of resolve_body:

uvx uncoded refs resolve_body --in src/uncoded/body.py

How agents use it

Agents load the navigation skills and follow this protocol once uncoded is set up:

1. Load the orientation artefacts. Read .uncoded/namespace.yaml to see every symbol at a glance. When doc-roots is configured, also read .uncoded/docs.yaml, the heading outline of all docs. Headings are literal text. Use Read or grep to navigate to a section.
2. Read the relevant .pyi stubs to understand imports, signatures, constants, and class members.
3. Run uvx uncoded body <name_path> --in <relative_path> when they need implementation detail for a specific symbol.
4. Run uvx uncoded refs <name_path> --in <relative_path> to find every reference to a symbol: callers, dead-symbol checks. See Find references to a symbol for detail.
5. Edit a symbol using Edit with uncoded body's output as old_string.
6. Rename across the codebase using uncoded refs to enumerate every site, then Edit at each.
7. Safely delete by running uncoded refs first. The output must be empty. Then Edit to remove.

Each tool owns one job. uncoded provides the stable map and signature index, code through namespace.yaml and docs through docs.yaml. uncoded body resolves a symbol's source body. uncoded refs maps every reference. Agents do not grep, guess line numbers, or do offset arithmetic.

Coherence review

AI coding agents tend to leave codebases in an incoherent state:

• names that no longer match behaviour
• docstrings that describe stale signatures
• dead symbols
• pattern changes applied in some places but not others

uncoded sync installs an /uncoded-coherence-review skill that runs a structured diagnostic sweep to find these problems.

Invoke it in Claude Code:

/uncoded-coherence-review

The review works in four sweeps:

1. Orient: loads namespace.yaml and forms a vocabulary map.
2. Lexical: scans the namespace for naming inconsistency: concept duplication, qualifier accretion (_v2, _legacy, _final), vocabulary islands, name collision with drift.
3. Promissory: checks each public symbol's name / signature / docstring triple for internal disagreement. Names and signatures come from the stub. Docstrings come from uncoded body.
4. Structural: checks for boundary violations (private symbols imported across modules), overgrown public surfaces, cross-domain imports, and zero-reference public symbols.

The review saves a timestamped Markdown report to .uncoded/reviews/, with verbatim evidence and a confidence level (high / medium / low) for each finding. The review only reports. The human decides what to follow up.

Upgrading from v1

Version 2.0.0 replaces injection with skills. In v1, uncoded sync always injected navigation guidance into AGENTS.md/CLAUDE.md. In v2 it ships as on-demand skills. Agents load them when relevant. Four manual steps after upgrading:

1. Remove old marker blocks from your AGENTS.md and CLAUDE.md. Look for and delete these blocks:

   <!-- uncoded:start ... -->
   ...
   <!-- uncoded:end -->
   

   and

   <!-- uncoded:docs:start ... -->
   ...
   <!-- uncoded:docs:end -->
   

   uncoded no longer manages these sections. Leaving them in place is harmless but they are now dead markup.

2. Update any skill pointer that references coherence-review to uncoded-coherence-review. The coherence review skill was renamed with the uncoded- prefix to match the navigation skills.

3. Remove the instruction-files config key if your pyproject.toml or .uncoded.toml has it. uncoded no longer reads this key. Leaving it in place causes no error.

4. Restore always-on navigation if you want v1 behaviour back. Add these lines to your AGENTS.md and CLAUDE.md:

   ## Before you start
   
   - Load the `uncoded-code-navigation` skill before searching, reading or editing any code.
   - Load the `uncoded-doc-navigation` skill before searching, reading or editing any docs.
   

Contributing

See AGENTS.md.