Register an entity in the identity tables. Creates INTERNAL (hash → id), EXTERNAL (id → hash), and NODE_TYPES (id → type) entries. Returns existing i

Rename a file or directory.

Resolve the agent author for a turn change. Looks up the user's default identity and derives an agent author with a `+tag` email. Falls back to a pla

Load candidate bodies from the vault, score, and rank them.

Attempt to resolve conflicts using the semantic merge engine. Handles two kinds of conflict: 1. **Cyclic conflicts** — multi-vertex SCCs where Tarja

Resolve the destination path. If destination is a directory, append the source filename.

Resolve the best available embedding provider from environment.

Extract the identity name from a remote URL alone (no server config). Tries URL userinfo first (`bob@host`), then the subdomain (`bob.host`). This is

Resolve the identity name to authenticate as. Priority: 1. An explicit override (the `--identity` flag). 2. URL userinfo (`http://bob@host/...`). 3.

Resolve the effective server config, honouring the optional name override. Resolution order: 1. `server_override` (from `--server <name>` CLI flag) 2

Resolve the workspace slug for a command, with fallback to the org-scoped default workspace from the **active** server profile. Loads global config,

Compute a row with an explicit verifier keypair (no global store).

Inner runner that takes the slug-verification step as a parameter. Splitting this out lets tests inject a deterministic verifier (succeed / fail) wit

Inner runner that takes the slug-verification step as a parameter. Splitting this out lets tests inject a deterministic verifier (succeed / fail) wit

Lowercased, deduplicated terms using KG FTS rules plus a small allowlist of meaningful short technology names. Exact token matching prevents substring

Node id for a session ledger.

Set the CRDT build statistics.

Set the current view (internal, does not update working copy). Update the view pointer on disk without materializing. This updates both the in-memor

Set the inode.

Attach the managed-run context for this hook invocation (see [`ManagedRunContext`]).

Set the AI vendor and model.

Returns `true` for machine-generated files (lockfiles, checksums, bundled output) that should be treated as opaque blobs — skipping CRDT tokenization

Strip markdown code block wrappers from a JSON string. Claude sometimes wraps JSON in ```json ... ``` blocks despite being asked not to. This strips

Create a temporary directory for testing.

Convert this entry to a Node. Respects the `tagged` field: tagged entries become `Node::tag`, regular entries become `Node::change`.

Convert the accumulated graph to a content-addressed `ProvenanceGraph` suitable for storage in the Atomic graph alongside changes and attestations. P

Convert to retrieve options for the alive graph module.

Tokenize a single file's content. This runs on a rayon worker thread for parallel regeneration.

Store mtime + size + content hash for a batch of files in a single transaction. This populates the file index so that `status` can compare file metad

Reconcile lifecycle metadata for a session record. Called from agent session start/end hooks. Creates the record if the session has no ledger entries

Ensure a grant mutation targets a concrete user or team. `Everyone` is emitted by Storage when listing public grants, but the mutation endpoints requ

Validate a session ID to prevent path traversal. Rejects IDs containing `..`, `/`, `\`, or null bytes.

Embed a single vault entry using the provided embedding function. Chunks the content by heading/paragraph, computes embeddings via `embed_fn`, and st

Delete an unstarted backlog intent. This is intentionally conservative: only backlog intents with no linked goals can be deleted. Started work should

Generic verify over a JSON-LD value — the same three checks as the typed path: (1) the content hash recomputes over `hashing_view`, (2) the signature

Sets whether to use code-aware tokenization.

Sets whether to use code-aware tokenization. When enabled, the tokenizer recognizes multi-character operators, string literals, numeric literals, and

Builder: set the dry-run flag.

Builder: set the `--force` flag.

Builder: set the output format.

Builder: set the starting sequence number.

Builder: set full hash display.

Set the maximum file size for diffing. Files larger than this are treated as binary. # Arguments `size` - Maximum size in bytes, or `None` for no l

Set the modification time.

Builder: set the name-only flag.

Builder: set the no-color flag.

Builder: set whether to hide untracked files.

Builder: set the remote name or URL.

Builder: set the remote state.

Builder: set tags-only filter.

Builder: set the timeout in seconds.

Add a warning.

Add another `PhaseTokens` into `self` (used for running totals).

Add a credit to the statistics.

Adds a branch operation with its ID.

Add a directory item.

Associate an inode update with a graph_op. When the change is applied locally, this update will be used to maintain the tree/inode database tables.

Adds a leaf operation with its ID.

Adds a new line to a file and returns its branch ID. # Arguments `trunk_id` - The file to add the line to `after` - The branch to insert after (None

Adds a line to this file.

Record a missing up-context position.

Add a pending edge to be created.

Create statistics for an added file. # Arguments `path` - The file path `lines` - Number of lines in the new file

Set the human-readable agent display name.

Aggregate tool usage from condensed entries.

Create options that include everything.

Set whether to allow conflicts.

Append content to the buffer and return the position range. # Arguments `data` - Content bytes to append # Returns A tuple of (start_position, end

Append content to the contents blob. Returns the starting position of the appended content.

Persist deferred operations atomically. The caller holds pristine's write transaction, which serializes journal writers across processes.

Append an LLM response node — the agent's final answer for the turn. Created at turn end from the agent's closing message: the stop payload's respons

Truncate bodies so their combined length fits `budget_chars`. Start with an even allocation, then give unused capacity from short bodies to higher-ran

Independent oracle: base with the given (index → new line) replacements.

Fold messages and parts into [`TurnData`]. The current turn starts at the last user message; reasoning, response, and step statistics are scoped to t

Assert content after a specific change matches.

Run `atomic <args>` inside `repo_dir` with `HOME` pointed at `home_dir` so the identity store resolves to a test-owned location.

Attach a Bearer JWT auth header to the remote config. `identity_override` — if provided, this identity name is used directly, bypassing URL-based inf

Lift+attest a stored memory with the given keypair.

A minimal, fully attested Memory that conforms — the base for mutation.

Build inputs for a minimal, liftable intent and attest them into a node.