Scan the vault working copy for changed files. Walks `.vault/` and compares each markdown file against its stored entry in redb. Returns a list of pa

Verify that the declared state equals the fold of the change log.

Walk the directory tree recursively. Yields all files (not directories) under the given path, respecting ignore patterns. The `.atomic` directory is

Sets the common ancestor vertex via builder pattern.

Attach a header to this entry.

Builder: set the number of context lines.

Mark that this change has an unhashed section. Automatically sets the `HAS_UNHASHED` flag.

Write a conflict marker line. The format is: `MARKER ID [HASH]` followed by a newline.

Add a conflict to the result.

Add a line to this graph_op.

Adds a trunk operation.

Add an up-context position (predecessor). Up-context vertices are the predecessors where new content will be inserted after.

Appends content and returns the byte range.

Apply this alignment to a string within a given width. # Arguments `text` - The text to align `width` - The total width to fill # Returns A string

Recursively apply the agent-native help layout to a command and every one of its (transitive) subcommands. clap does not propagate `help_template` to

Set whether to insert dependencies automatically.

Returns the canonical string representation of this hook type.

Returns the token content as a string (lossy UTF-8 conversion).

Join lines with '\n' and a trailing newline (the well-supported shape).

The tracked-vault path for a memory's attestation: `attestations/memory/<sanitized-id>/attested.md`. NOTE the `attestations/memory/` sub-namespace: a

Build the provenance. # Panics Panics if vendor or model is not set.

Build a [`StorageClient`] and return the resolved org slug alongside it. Useful for commands that also need to resolve org-scoped state (e.g. per-org

Build (or rebuild) the content search index for the repository. Indexes files in the working copy while respecting `.gitignore`, `.ignore`, `.atomici

Build history options from command settings. Converts the command's settings into `HistoryOptions` for querying the repository. # Returns `HistoryO

Collect all files in a directory for tracking. This walks the directory tree and returns paths relative to the given root. Files matching `.atomicign

Compress all chunks in parallel using rayon and zstd. Each chunk is compressed independently on a rayon worker thread. This utilizes all available CP

Ensure the workspace directory for a view exists. Creates `.atomic/workspaces/<view_name>/` and any intermediate directories. This is called from `i

Extract entities from a source file. Automatically selects the right parser based on the file extension. Returns an empty list if the language is not

Format a timestamp for display. Converts a UTC timestamp to local time and formats it in a human-readable format. # Arguments `timestamp` - The UTC

Format a timestamp in a relative format (e.g., "2 hours ago"). This provides a more conversational representation of time that's easier to understand

Set whether to include deleted vertices. When true, vertices marked as deleted will be included in the graph. This is useful for showing conflict con

Insert a change with automatic dependency resolution. This method attempts to insert a change and all its missing dependencies. Dependencies are inse

Check if this replacement has any effect.

Iterate over all attestation hashes on disk.

Get the number of changes in the store.

List all tracked files in the repository. # Example ```rust,ignore for file in repo.list_tracked_files()? { println!("{}: inode {}", file.path.displ

Load a provenance graph from the repository by hash.

Create a change with the given content bytes and return its hash.

Build a `SerializedGraphEdge` with the given flags and arbitrary but deterministic dest / introduced_by values.

Set the maximum number of vertices to process. # Arguments `max` - Maximum span count # Example ```rust use atomic_core::output::repo::FileOutputO

Helper: build a `MockGraph` with one vertex that has every valid edge kind.

Create a new name conflict. Name conflicts occur when a file has been renamed by concurrent changes.

Get the text content of a node.

Output graph content with semantic-merge resolution. This is the merge-aware counterpart of [`output_graph_content`]. For every SCC whose lead verte

Peek at the next section's type without consuming it. Reads the section header from the source and stashes it internally. The next call to [`next_sec

Get the current byte position in the original content.

Set the prefix filter. # Arguments `prefix` - Path prefix to filter # Example ```rust use atomic_core::output::repo::TreeCollectOptions; let opts

Set the prefix filter.

Get the public key as a base32 string.

Record a skipped file. # Arguments `path` - The path of the file that was skipped # Example ```rust use atomic_core::output::repo::OutputOutcome;

A fresh repo+vault.

Resolve the effective server config mutably, honouring the optional name override. Mirrors the resolution order of [`resolve_server`](Self::resolve_s

Compute a single row using an explicit verifier keypair (no global store). Reads the row's kind tag from the manifest, exactly as `build_rows` does.

Execute the status command. This method: 1. Finds and opens the repository 2. Computes the working copy status 3. Displays the status in the requeste

Serialize the attestation to bytes. Format: `[MAGIC: 4 bytes][postcard payload]` The hash is computed over the entire serialized output.

Set the first prompt if not already set. Truncates to MAX_PROMPT_LENGTH. Also updates `current_prompt` on every call so the change message reflects th

Set the position.

Split a set of changes out of a view into a new Draft view. This is a pure metadata operation guarded by a reverse-dependency check: a change cannot

Store a memory via the GENERIC vault path (as `memory write`/attest do).