Normalize a path relative to the repository root.

The normalized intent id used to key BOTH the tracked vault attestation path and the legacy `.atomic` sidecar dir, so the dual-read fallback lines up

Open or create a pristine database at the given path This will create all necessary tables if they don't exist.

Open or create an identity store at the specified path.

Convert [`ToolMessage`] list into OpenAI's messages array.

Parse a change identifier from a string. # Arguments `s` - The identifier string # Returns The parsed `ChangeIdentifier`. # Parsing Rules - If t

Parse an author string in the format `"Name <email>"` or just `"Name"`. # Arguments `s` - The author string to parse # Returns A tuple of (name, o

Parse author string into name and email.

Parse a git commit message into subject and description.

Parse the standard embedding API response format (shared by OpenAI and Voyage).

Parse a git config file's `[user]` section for `name` and `email`. Only fills in values that are currently `None`, so local config values take preced

Extract inline directives (`:name[label]{attrs}`) from running prose. Recognition rules keep prose safe: - the `:` must sit at a word boundary (start

Parse a PR/MR number from a commit message. Supports multiple forge formats: - GitHub: `(#42)` or `Merge pull request #42 from ...` - GitLab:

Parse and verify a remote manifest, mapping failures to remote errors. The declared state must equal the fold of the log — a remote that sends an inc

Parse and verify a view manifest downloaded from the remote. Validates three things before the manifest is trusted: 1. The text parses structurally

Parse a stash reference (e.g., "stash@{0}", "0", or view name).

Interpret the registration response's tenancy signal. `mode: "single"` (server v1.4.0+) marks a single-tenant deployment and carries the org `role` t

After materializing the current view, list any conflicted files inline so the user does not have to run a second command to find them.

Print the outcome of a cross-view insert operation.

Print a reasoning summary in a readable format.

Set the schema profile identifier. Use [`super::SHERPA_PROFILE`] for Sherpa-structured graphs. Omit for generic agent graphs — `profile` defaults to

Get the corresponding public key

Rebuild session indexes from stored provenance graphs. Idempotent: existing `(session, provenance)` pairs are skipped, so a rebuilt repository never

Record a successfully applied change.

Returns the list of files that were recorded in this turn.

Convenience: map a [`atomic_remote::RemoteError`] to a [`CliError`].

Remove all Atomic hooks from a matcher list. Preserves non-Atomic hooks. Removes empty matchers (those with no remaining hooks after Atomic hooks are

Rename a remote. # Arguments `old_name` - The current name of the remote `new_name` - The new name for the remote # Errors Returns an error if: -

Render a clap parse failure as `key: value` lines. A pure function returning a `String`, so the whole failure surface is unit-testable without spawni

Render the prompt-ready markdown block. Empty input renders to an empty string so callers can prepend unconditionally.

Create a repo+vault and a single intent; return (repo, normalized id, lift inputs for the stored intent).

Build a report where a single intent A (installed with `body_a`) is reached by a candidate that modifies every path in `files`. Each path is created +

Look up an agent adapter by name, returning an error if not found. This is a convenience method for CLI commands that need to validate the agent name

Open a repository or return a user-friendly error. This is a convenience wrapper around [`open_repository`] that provides more context in error messa

Resolve a node_id that may be a `$variable` reference. If it starts with `$`, look up the binding and extract node IDs. Otherwise return it as-is.

Resolve the target path to an absolute path. If the path is relative, it's resolved relative to the current working directory.

Convert an external position (with Hash) to an internal position (with NodeId). This is the bridge between the serialized change format (using hashes

Resolve the target path for cloning. If `path` is provided, uses that. Otherwise, infers from the URL. # Arguments `url` - The remote URL `path` -

Resolve the current identity for vault operations. Resolution order: 1. Atomic identity store (default identity) 2. Git config (user.name + user.emai

Restore a single file according to its status. - `Added` (tracked but not recorded): undo tracking. The file stays on disk and becomes untracked, so

Retrieve content with options. Like `retrieve_content`, but allows configuration via options. # Arguments `txn` - Transaction providing graph acces

Builder: set reverse order.

Build a report where work intent A (author `WORK_AUTHOR`, touching `a.txt`) is optionally covered by a review intent R. `review` is `(review_author, r

A report fixture whose finding message carries HTML/JS metacharacters, so escaping can be asserted.

Save remote configuration to a config file. This preserves other sections in the config file and only updates the `[remotes]` section. # Arguments

Save the store configuration.

Get the session directory for provenance graph storage. Returns `{sessions_dir}/{session_id}/` — a subdirectory alongside the session's JSON file. Th

Set the default remote.

Set the encoding.

Set the inode.

Set the change kind.

Sets the trunk's path (for move operations).

Check if a path should be ignored during tracking, with optional ignore rules. This is the full version that accepts optional [`IgnoreRules`] for pat

Get the Merkle state as a base32-encoded string.

Get the conversion statistics.

Return statistics about the table for debugging and logging. # Examples ```rust use atomic_core::change::format_v3::HashDedupTable; let mut table =

Returns a human-readable suggestion for how to fix this error. This is intended for CLI error reporting where a "did you mean?" style hint can guide

Make prior atomic renames/removals in `.atomic` durable before a coupled database transition is allowed to advance. Directory fsync is available on Un

Convert to file output options.

Format this entry as a protocol line.

Serialize to the full JSON-compatible representation.

Node id for a todo. Agent-provided IDs are only stable within their session, so qualify them with that session. Generated turn-local IDs are already f

Set the generic todo snapshot captured at turn end.

Get all tracked paths under a directory prefix. # Arguments `txn` - A transaction (read or write) `prefix` - The directory prefix to search under

Advance the state machine to at least the given state. This handles the forward transitions: if we're in WritingMetadata and asked to write a SEMANTI

Compute the triage candidate set for `feature` relative to `target`. See the module documentation for the semantics of each field. # Errors Returns

Truncate a string for summary display, adding "..." if truncated.

Truncate a prompt to the given maximum length, adding "..." if needed.

Truncate a prompt string for display, preserving word boundaries where possible.

Node id for one turn row in a session ledger.

Remove a previously installed integration, guided by its receipt. Files the user modified since install are kept (and reported). Settings entries are

Limit changes to those up to and including a tag.