Set the number of SEMANTIC sections (one per modified file). Automatically sets the `HAS_SEMANTIC` flag if count > 0.

Set the agent identity for sessions created by this orchestrator. Called by the CLI hook handler after construction, before dispatching events. This

Set the detail field.

Builder: set files to restore.

Set custom metadata.

Builder: set summary.

Add a graph_op to this diff.

Add a graph_op to the recorded actions. # Arguments `graph_op` - The graph_op to add # Returns The index of the added graph_op (for associating in

Performs the analysis and returns the result. This is the main entry point for analyzing differences.

Build RecordOptions from command-line arguments.

Build AI provenance from CLI flags and environment variables. Environment variables take precedence over CLI flags for consistency with AI tool integ

Build the change message for a turn. Message priority: 1. If the prompt is meaningful (not a slash command, not too short), use it directly — the use

Compute the filesystem path for a change with the given hash. The path follows the two-level directory structure: `{changes_dir}/{prefix}/{full_hash}

Compute the new Merkle state after applying a change. The Merkle state is computed incrementally: `new_state = Hash(old_state || change_hash)` This

Compute the output order using Tarjan's SCC algorithm. This function: 1. Runs Tarjan's algorithm to find all SCCs 2. Builds the conflict tree 3. Iden

Format conflict content in bold red. Use this for conflict markers or conflicted file indicators.

Convert a SemanticDiff to FileOps. # Arguments `diff` - The semantic diff to convert `path` - The file path # Returns A `FileOps` containing all t

Converts a file addition with content to CRDT operations. This generates: - `TrunkOp::Create` for the file - `BranchOp::Insert` for each line - `Leaf

Get the number of changes unrecorded.

Create a named tag on the current view at the current sequence.

Create a simple test FileAdd graph_op

Set the email address.

Produce the multi-line outdated message for a given source. Pure so the unit tests can match on substrings.

Get the default identity ID.

Get the recorded content for a tracked file. This method builds a **change filter** that defines the current view's content perspective, then retriev

Simple hash-based "embedding" for testing purposes. Produces a deterministic vector from text content using character frequency analysis. NOT suitabl

Check if this format is a single file.

Check if a node has a `pub` visibility modifier.

Check if the push was successful (no failures).

Check if a path is tracked. # Arguments `txn` - A transaction (read or write) `path` - The normalized path string

Get the number of collected files.

Load an identity by name.

Load remote configuration for this repository. # Returns The remote configuration, which may be empty if no remotes are configured. # Errors Retur

Helper to create a test inode.

Helper to create a test span.

Print a blank line for visual separation.

Execute the init command. This method: 1. Resolves and validates the target path 2. Validates the view name 3. Creates the directory if it doesn't ex

Save a change to the repository. The change is serialized and written to the `.atomic/changes/` directory using a content-addressed two-level directo

Save learnings to the agent's context file. If the file doesn't exist, creates it with the learnings section. If the file exists but has no learnings

Convert a [`ProvenanceGraph`] into a [`TraceRecord`] suitable for appending to `.agent-trace/traces.jsonl`. `root` is the repository root used for co

Serialize to a compact binary blob via postcard.

Iterate over untracked files.

Extract and store KG data for a vault entry in one step.

Set a change filter for view-aware output.

Builder: set the initial view name.

Open a file for writing, creating it if necessary.

Write this header to a writer. Writes exactly 64 bytes. # Errors Returns an I/O error if the write fails.

Add a single file to tracking. This is the low-level function that actually modifies the database. It does NOT check if the file exists on disk or is

Append a patch proposal node (change recorded). Returns the new node's ID.

Run `atomic <args>` inside `dir`.

Collect all change `NodeId`s visible from a view, including parent views. For **draft** views this walks the full overlay chain (other draft ancestor

Get a reference to the underlying database.

Create a Delete operation.

Compute the diff between two sequences of lines. This is the main entry point for diffing. It takes two slices of [`Line`]s and returns a [`DiffResul

Diff two snapshots to produce a `TurnChanges`.

Execute a query plan against a repository.

Builder: set format.

Get the inode for a tracked path. # Arguments `txn` - A transaction (read or write) `path` - The normalized path string

Check if this is the repository root.

Returns this trunk's branches in **file order** — top-of-file first. Iteration over `TRUNK_BRANCHES` alone returns branches in `(change_id, branch_id

Get the number of entries (files + directories).