docs: correct claims the code does not back

[r0h1tb]

Description

Audited README, AGENTS.md, CONTRIBUTING.md and docs/ against the current
source. Every change below was checked by running the thing it describes.

Commands and flags that don't exist as documented

• README's CLI list had 11 of 20 commands. create-database, call-graph,
  symbol-impact, blocks, lambdas, summarize, analyze-stacktrace,
  cache-stats and stats were undocumented.
• ast-rag update <path> → Missing option '--from-commit'. Both
  --from-commit and --to-commit are required.
• ast-rag sandbox <lang> <cmd> → FileNotFoundError: workdir does not exist.
  The second positional is workdir; the command goes in --cmd.
• QUICKSTART used --from/--to and a --current-branch that doesn't exist.
• query --verbose and sig --kind → No such option.
• QUICKSTART used callers to "find what it calls"; that's
  call-graph --direction callees.
• AGENTS.md described workspace as "Update from git diff"; it shows
  uncommitted changes.

Python API examples that raise

• get_diff(from_commit=, to_commit=, file_path=) — real signature is
  get_diff(repo_path, from_commit, to_commit=None, limit, offset), no
  per-file filter.
• full_index(driver, path, commit=) — real is
  full_index(driver, nodes, edges, commit_hash=...) -> None.
• update_from_git(root=, from_commit=, to_commit=) — real kwargs are
  repo_path, old_commit, new_commit.
• index_directory, ast_rag.graph_schema, ast_rag.embeddings and
  ast_rag.benchmarks.evaluator do not exist.
• find_references returns a dict of dicts, not objects with .node.
• ASTNode.node_type is kind.
• ProjectConfig.model_validate_json("ast_rag_config.json") takes JSON text,
  not a path.

Config

• Bare NEO4J_URI / QDRANT_URL / EMBEDDING_URL are read nowhere. The real
  set is the six AST_RAG_* vars in cli.py:132-137; there is no
  embedding-URL override.
• The example set remote_url with no dimension, which raises
  EmbeddingConfig.dimension must be set when using remote_url. Embeddings are
  local by default and docker-compose.yml starts no embedding server.
• model_name default is BAAI/bge-m3, not bge-m3.
• "Tune thresholds in embeddings.py" — no such module. The real knobs are
  vector_weight/keyword_weight.
• Nothing documented the [mcp] extra, without which ast-rag-mcp and
  ast-rag-watch are on PATH but fail to import.

Shell scripts that never existed

./scripts/index-remaining.sh and index-sequential.sh are referenced across
four docs. git log --all -- 'scripts/*.sh' is empty and scripts/ contains
only README.md.

Graph schema

Both ID formulas were wrong — the node ID includes project_id and the edge ID
includes dep_kind:raw_type_string:confidence. Verified by computing both
hashes. Added the missing Block label and TYPES/DEPENDS_ON/
CROSS_FILE_CALL edges, and noted that HAS_PARAMETER, VIRTUAL_CALL and
LAMBDA_CALL are declared and indexed but never emitted.

Roadmap drift

summarize shipped but was listed as planned; Go was still under "More
languages" in README and CONTRIBUTING after landing in #17.

Related Issue

None — a sweep. #66 was already fixed and closed; only its roadmap half remained.

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update

Checklist

• My code follows the code style of this project
• I have added tests — documentation only
• All new and existing tests passed (unchanged: no source touched)
• I have updated the documentation accordingly
• I have run ast-rag evaluate --all — needs live services
• My changes generate no new warnings

Testing

No source changes. Commands and flags checked against ast-rag <cmd> --help,
API signatures and imports against the source, config fields against
dto/config.py and the EmbeddingManager guard, ID formulas by computing the
hashes both ways.

Not re-measured: the Phase-2 numbers themselves need live Neo4j and Qdrant.
git log -S "F1 Score" -- README.md dates them to 1852590, 2026-02-26, so
they are dated and marked as not re-measured rather than restated as current.
Also left alone with reasons: QUICKSTART's indexing-time estimates, the
roadmap rows with no evidence either way, and the SUMMARIZATION model
recommendations.

Three things left for you

• scripts/README.md documents both nonexistent shell scripts in detail, and
  README links it as "Indexing utilities". Needs deleting or rewriting — out of
  scope here.
• docs/STACK_TRACE_MAPPING.md is in Russian while AGENTS.md says
  documentation is English. A policy call, not a false claim; only its imports
  were fixed.
• AGENTS.md line 8 has a paste artifact: .qweAlways confirm documentation language preference.... Left as-is.

[lexasub]

docs/STACK_TRACE_MAPPING.md - it's not a big deal that it's in English. If it's a nuisance, you can translate it into English. typo in agents.md, it's best to fix it.