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

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

Get the file extension for this format.

Extract unhashed turn data from a change. Returns `None` if the change has no unhashed data or no `"agent_turn"` key.

Build a fake package in a tempdir: manifest + two files + a settings manifest. Returns (pkg_dir, dst_dir) tempdirs.

Get metadata for a file or directory.

Filter to a specific path prefix.

Recompute the contents hash after modifying contents.

Indices of unclassified tool-derived nodes grouped into sequences separated by structural boundaries (goals, patches, human gates, errors).

Find lines that appear exactly once in both sequences and match. Returns a list of matches sorted by position in the old sequence.

Finish a progress bar with an error message. This clears the progress bar and displays an error message in red. # Arguments `pb` - The progress bar

Return the 1-based line number of the first Atomic conflict-start marker (`>>>>>>>`) in `content`, or `None` if the content has no markers. This is t

Format condensed entries as human-readable text. Output format: ```text [User] Fix the auth bug in login.rs [Assistant] I'll fix the token validation

Format learnings as individual list items grouped by category. Only includes **Repo** and **Workflow** learnings. Code learnings (with file:line refe

Format entries for oneline output. # Arguments `entries` - History entries to format `hash_length` - Number of hash characters to display # Returns

Format the change for short output.

Build hunks from a diff result with context lines. This function groups diff operations into hunks with the specified number of context lines around

Gather candidate memory nodes from all seeds. Returns a map of memory node id -> accumulated candidate score. With no seeds at all, falls back to the

Generate diff operations between two content blobs. Converts content to lines and runs the specified diff algorithm. # Arguments `old_content` - Ol

Get the default remote, if one is configured. Returns the first remote marked as default, or "origin" if it exists and no other default is set. # Ex

Get the raw contents of a file. Returns `None` if the file doesn't exist or is a directory. # Example ```rust use atomic_core::output::Memory; let

Get the message for the revised change.

Get the Merkle state at a given sequence number.

Get the global configuration directory. Resolution order: 1. The `ATOMIC_CONFIG_DIR` environment variable, if set — used verbatim as the config direc

Wrap an `atomic agent hooks …` invocation in the shell guard that installed hooks run behind. The hook must only fire where Atomic's graph is reachab

Filter by identity type.

Set whether to include deleted content.

Set whether to include deleted vertices. # Arguments `include` - Whether to include deleted content # Example ```rust use atomic_core::output::rep

Initialize the embeddings table.

Creates a line insert operation with leaf operations. # Arguments `branch_id` - The branch ID for this new line `after` - Insert after this branch I

Mark a vertex as "skip" — it belongs to a resolved SCC but is not the lead vertex.

Returns true if the token is alive (not deleted).

Check if this status represents a change that needs to be recorded. Returns `true` for statuses that indicate uncommitted changes.

Check if the builder is empty (no changes recorded). # Returns `true` if no hunks have been recorded yet.

Check if no files were collected.

Check if the tracker is empty.

Returns `true` if no layers are selected.

True if `path` lives in an Atomic-internal directory that must never be enriched into the knowledge graph or indexed for content search. Covers the a

Determine if a declaration is exported (publicly visible). Walks the immediate children of the declaration node looking for access-level modifiers. S

Check if this error is because a path is ignored

Returns the number of selected layers.

Get the number of signatures.

Lift the given inputs into a canonical `MemoryNode`, mapping a lift failure (missing `uid`, missing `memoryKind`, …) to a clean argument error.

List tracked files eligible for knowledge-graph enrichment. Filters [`list_tracked_files`](Self::list_tracked_files) to exclude: - Atomic/Git interna

List all tracked files. # Arguments `txn` - A transaction (read or write) # Returns A vector of all tracked files and directories.

Load an intent's attestation sidecar and classify it against the current source (`inputs`). A missing sidecar is `None`; a corrupt/malformed one is tr

Create a short prefix from a session ID for use in node IDs. Takes up to the first 8 characters. If the session ID is a UUID, this is the first segme

Check if an identity matches this filter.

Merge another outcome into this one. This is useful when collecting results from multiple output operations (e.g., outputting different subtrees). #

Merge results from a file output.

Merge new items into existing section headings without duplicating headings. If `### Repo` already exists in the section, new repo items are appended

Merge `source` paths into `target`, deduplicating.

Iterate over modified files.

Iterate over modified lines.

Normalize a path by resolving `.` and `..` components. Unlike `canonicalize()`, this doesn't require the path to exist.

Parse the algorithm string into an Algorithm enum.

Parse the algorithm string into an Algorithm enum.

Parse the author string into an Author struct.

Parse a changelist response into entries.

Check if a change ID passes the filter. Returns true if: - No filter is set (all changes pass) - The change_id is ROOT (NodeId(0), always passes) - T

Add a permission.

Print a section header. Use this to visually separate different sections of output. # Arguments `title` - The section title # Example ```rust,ign

Print the status in short (porcelain) format.

Process a deletion. # Arguments `old_index` - Starting line in old content `new_index` - Position in new content (deletion point) `old_len` - Number

Returns the prompt truncated to `max_len` characters. Useful for display purposes (commit messages, UI previews). Returns `None` if no prompt is pres

Record a single deleted file. Creates a deletion graph_op for a file that no longer exists in the working copy. # Arguments `detected` - The detect

Record a successfully downloaded change. Increments the download counter. # Example ```rust use atomic::commands::clone::types::CloneProgress; let