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.

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

Delete a vault entry by path. Also updates the manifest.

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

Extract KG nodes and edges from a vault entry. Returns `(Vec<KgNode>, Vec<KgEdge>)`. Does **not** store them — call `vault_store_kg` for persistence.

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

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 files to diff.

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 state.

Builder: set tags-only filter.

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

Aggregate tool usage from condensed entries.

Create options that include everything.

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.

Assert content after a specific change matches.

Build a compact text representation of KG nodes and edges for the LLM prompt. Groups nodes by kind and renders edges as relationship sentences. Hard

Build an identity filter from the command arguments.

Build the summarization prompt from the condensed transcript.

Build the HTTP remote configuration. `identity_hint` — explicit identity name to use (from `--identity` or `RemoteEntry.identity`). When `None`, fall

Build the HTTP remote configuration. Creates an `HttpRemoteConfig` with the timeout and security settings specified by the user.

Build the HTTP remote configuration. `identity_hint` — explicit identity name to use (from `--identity` or `RemoteEntry.identity`). When `None`, fall

Build a tree structure from flat paths. Organizes items into a hierarchical structure by parent-child relationships. # Arguments `items` - Flat lis

Get the path where a change file should be stored. Changes are stored in a two-level directory structure based on their hash: `.atomic/changes/AB/CDE

Iterate over only the change operations (non-Equal).

Chunk text by heading boundaries, then by paragraph, respecting a maximum token budget per chunk. Strategy: 1. Split on `#` headings (any level) 2. I

Split content into chunks and return chunking statistics. This is the same as [`chunk_content`] but also returns [`ChunkingStats`] for logging and pr

Set whether to collect directories. # Arguments `collect` - Whether to include directories in results # Example ```rust use atomic_core::output::r

Set whether to collect files. # Arguments `collect` - Whether to include files in results # Example ```rust use atomic_core::output::repo::TreeCol

Collect all change `NodeId`s inserted into a view into a `HashSet`. This is the canonical helper for building a **change filter** — the set of change

Find the length of common prefix and suffix between two sequences, applying the **suffix-limiting heuristic** used by the display path. This optimiza

Convert an `Insertion<Option<Hash>>` to a [`CompactInsertion`].

Compare content with size limit check. Like `compare_content`, but treats files over the size limit as binary. # Arguments `old_content` - Content

Compute the USD cost for a pair of token counts. Uses [`COST_PER_M_INPUT`] and [`COST_PER_M_OUTPUT`] so every layer that touches token accounting pro

Compute token-level changes between two lines. This is the core of the token-level diff - it compares the tokens of two lines and produces a sequence

Create token changes for a line that was entirely added.

Remove a file from the FILE_INDEX. Call this when a file is deleted (e.g., during git import cleanup) so that `status` doesn't show it as a stale ent

Set the delegating identity (for delegated identities).

Delete a change from the store. Removes all entries for this change from CHANGE_META, CHANGE_GRAPH, CHANGE_SEMANTIC, CHANGE_CHUNKS, and CHANGE_UNHASH

Create statistics for a deleted file. # Arguments `path` - The file path `lines` - Number of lines in the deleted file

Deserialize the payload from postcard format. Convenience wrapper around [`postcard::from_bytes`] that handles the error conversion. # Type Paramete

Detect the encoding of content. # Arguments `content` - The content to analyze # Returns The detected encoding.

Walk up from `start` looking for a [`SANDBOX_POINTER`] file. If found, return `(working_root, canonical_root, view)`.

Determine the install source for a binary at `current_exe`. Manifest is consulted first under the trust gate (canonicalized path must match current_e

Compute an edit script transforming `old` into `new` at the token level. Returns a sequence of [`EditOp`]s. The algorithm uses dynamic-programming LC

All edges.

Mark the end of the current turn and increment the turn count. Returns the turn number that just completed (1-indexed).

Ensure all directories in a path exist.

Add an exclude pattern. # Arguments `pattern` - Pattern to exclude (simple prefix matching) # Example ```rust use atomic_core::output::repo::TreeC

Add exclude patterns.