dodder-usage

name	Dodder Usage
description	Guides day-to-day dodder and der operations including creating zettels, querying and filtering objects, checking out working copies, organizing content, syncing with remotes, and managing tags, types, and dormant objects. Activated by requests to create, edit, organize, query, show, checkout, checkin, push, pull, sync, tag, or otherwise operate on dodder repositories.
triggers	["create a zettel","organize zettels","dodder checkout","dodder push","dodder pull","query dodder","find zettels","sync dodder","tag a zettel","edit a zettel","dodder commands","der","dodder status","dodder show"]

Dodder Usage

dodder and der

dodder and der are the same tool. der is a shortname alias that behaves identically. Every command and flag documented here works with either binary. madder is a separate low-level tool for internal repository operations and is not covered by this skill.

Creating Content

Create new zettels with dodder new. By default, the command creates one empty zettel and opens it in the configured editor ($EDITOR or $VISUAL).

dodder new                         # create one empty zettel, open editor
dodder new -edit=false             # create one empty zettel, no editor
dodder new -edit=false file.txt    # import content from a file
dodder new -tags project -type md  # set metadata at creation time
dodder new -count=5 -edit=false    # create 5 empty zettels at once
dodder new -shas                   # treat arguments as already-checked-in blob SHAs
dodder new -organize               # create zettel(s), then open organize UI
dodder new -delete                 # delete source file after import

The -filter flag accepts a script path that transforms each input file into the standard zettel triple-hyphen format before import.

When creating from files, pass one or more file paths as positional arguments. Each file becomes a separate zettel with its content as the blob. Combine with -description, -tags, and -type to set metadata on all created zettels.

Viewing and Querying

Use dodder show to query and display objects. The default output format is log (one-line summary per object). Query syntax uses positional arguments with genre, sigil, tag, and type selectors.

dodder show :z                     # all zettels (latest versions)
dodder show one/uno                # specific zettel by ID
dodder show -format text one/uno   # detailed multi-line view
dodder show -format json one/uno   # JSON output for scripting
dodder show tag-name:z             # zettels carrying a specific tag
dodder show !md:z                  # zettels of type md
dodder show :?z                    # include dormant/hidden zettels
dodder show :t                     # all types
dodder show :e                     # all tags
dodder show :z,t                   # zettels and types
dodder show :r                     # all repos
dodder show -before 2024-01-01 :z  # zettels before a date
dodder show -after 2024-01-01 :z   # zettels after a date
dodder show -repo remote-id :z     # query a remote repository

The -format flag supports log (default, one-line), text (detailed multi-line), and json (machine-readable).

Use dodder cat for raw blob output, and dodder last to display the most recently changed objects from the latest inventory list.

Configuration

Repository configuration is not a queryable object. It cannot be selected with show or any genre filter; a query naming konfig or config errors with config is no longer an object; use show-config / edit-config. Use the dedicated commands instead.

dodder show-config                 # print the latest config (bare TOML)
dodder show-config <digest>        # print a historical config state's blob
dodder show-config -history        # list config history (oldest to newest)
dodder edit-config                 # open the config TOML in the editor

edit-config opens the bare config TOML in $EDITOR; on save it records the new state in a repo-local config log. Configuration is repo-local and is not transferred by push or pull. A clone seeds the new repository's config from the source.

Editing

Open a zettel for editing in the configured editor with dodder edit. The -mode flag controls what to edit.

dodder edit one/uno                       # edit metadata and blob (default)
dodder edit -mode metadata-only one/uno   # edit metadata only
dodder edit -mode blob-only one/uno       # edit blob only
dodder edit -delete one/uno               # delete after editing
dodder edit -organize one/uno             # open organize after editing

After external edits (outside the editor), use dodder checkin to commit changes back to the store. checkin has two aliases: add and save.

dodder checkin one/uno                    # commit changes from working copy
dodder checkin -ignore-blob one/uno       # update metadata only, keep blob
dodder checkin -each-blob "cmd" :z        # run command on each blob
dodder checkin -tags project :z           # add tags during checkin
dodder checkin -type md :z                # set type during checkin
dodder checkin -delete :z                 # delete working copy after checkin
dodder checkin -organize :z               # open organize after checkin

Checkout and Working Copy

The checkout system syncs objects from the store to the filesystem. Use dodder checkout to materialize objects as files.

dodder checkout :z                 # checkout all zettels
dodder checkout one/uno            # checkout a specific zettel
dodder checkout -organize :z       # checkout then open organize UI
dodder checkout :?z                # include dormant objects

View the current state of checked-out objects with dodder status.

dodder status                      # show all checked-out objects and their state
dodder status one/uno              # show state for specific object

Remove checked-out files from the working directory with dodder clean.

dodder clean                       # remove unchanged checked-out files
dodder clean -force                # remove all checked-out files regardless of changes
dodder clean -organize             # open organize UI to select files to remove
dodder clean -recognized-blobs     # also remove recognized but not checked-out blobs

View differences between the store and working copy with dodder diff.

dodder diff                        # diff all checked-out objects
dodder diff one/uno                # diff a specific object

Organizing

dodder organize opens a text-based bulk editing interface. It generates a structured text file listing objects, which can be edited to rename, retag, retype, or reorganize objects. Changes are committed when the editor closes.

dodder organize :z                          # organize all zettels
dodder organize -mode output-only :z        # preview the organize file (stdout)
dodder organize -mode commit-directly :z    # apply changes from stdin, no editor
dodder organize -mode interactive :z        # open vim to edit (default for TTY)
dodder organize -filter script.lua :z       # transform via script
dodder organize tag-name:z                  # organize zettels with a specific tag
dodder organize !md:z                       # organize zettels of a specific type

The organize interface represents objects as a hierarchical text document. Move lines to change tag assignments, edit descriptions, and retype objects. Deleting a line from the organize file does not delete the object from the store.

Remote Sync

Dodder supports push/pull synchronization with remote repositories. Remotes are registered objects within the local store.

Add a remote

dodder remote-add remote:///path/to/repo remote-id

The first argument is the remote URI and the second is the local name. The -tags and -description flags set metadata on the remote object.

Clone a repository

dodder clone backup remote:///path/to/source     # new local repo "backup" (XDG-user)
dodder clone .backup remote:///path/to/source     # new local repo as .dodder in CWD
dodder clone -organize backup remote:///path/to/source !md:z  # filter what gets cloned first

Clone creates a new local repository and pulls all inventory lists from the remote. Additional query arguments filter what to clone. -organize opens an editable outline of the matched objects before pulling — delete an entry to exclude it (not supported over the websocket transport).

Push and pull

dodder push remote-id              # push local changes to remote
dodder pull remote-id              # pull remote changes to local
dodder pull-blob-store path config # pull blobs from a blob store

Push and pull transfer inventory lists and their referenced objects. Both commands accept query arguments to limit what to transfer.

Workspaces

A workspace is a directory linked to a dodder repository. It provides default tags, type, and query for operations within that directory.

dodder init-workspace              # create workspace in current directory
dodder init-workspace subdir       # create workspace in a subdirectory
dodder init-workspace -tags work   # set default tags for the workspace
dodder init-workspace -type md     # set default type for the workspace
dodder init-workspace -query "project:z" # set default query
dodder init-workspace -organize -parent /path/to/parent workspace-id # filter what gets pulled first
dodder info-workspace              # show workspace configuration
dodder info-workspace query        # show default query
dodder info-workspace defaults.tags # show default tags
dodder info-workspace defaults.type # show default type

When a workspace exists, checkin, new, and organize automatically apply the workspace's default tags. show uses the workspace's default query when no arguments are given. -organize on init-workspace opens an editable outline of the objects that would be pulled from the parent repo before initializing (requires -experimental-repo, the default).

Query Syntax

Queries are positional arguments passed to commands like show, checkout, organize, edit, and checkin. The syntax combines object IDs, genre selectors, sigils, tag filters, and type filters.

Syntax	Meaning
:z	All zettels (latest)
:t	All types
:e	All tags
:r	All repos
:b	All inventory lists
:z,t	Zettels and types
one/uno	Specific object by ID
tag-name:z	Zettels with a specific tag
!md:z	Zettels of a specific type
:?z	Including dormant/hidden

Sigil characters modify selection scope:

Sigil	Character	Scope
Latest	:	Current versions only (default)
Hidden	?	Include dormant objects
History	+	Include historical versions
External	.	Include checked-out/external objects

Refer to references/querying.md for the complete query syntax reference with compound queries, time filtering, and practical examples.

Working Copy vs Store

The .dodder/ directory (or XDG-based equivalent) is the store. It contains all blobs, inventory lists, indices, and configuration. The filesystem outside .dodder/ is the working copy.

• checkout syncs store to filesystem (read from store, write to working copy).
• checkin syncs filesystem to store (read from working copy, write to store).
• status shows the relationship between store and working copy.
• diff shows differences between the two.
• clean removes working copy files.

The store is always the source of truth. The working copy is ephemeral and can be fully recreated from the store at any time.

Tags and Types

Tags and types are first-class objects in dodder, each with their own IDs and metadata stored in the repository.

Tags organize and categorize objects, similar to labels. A zettel can carry any number of tags. Tags are referenced in queries by name (e.g., project:z matches all zettels tagged project).

Tag prefixes carry special meaning:

Prefix	Meaning
(none)	Regular tag
-	Dependent tag (implicit, derived from parent)
%	Virtual tag (computed, not stored directly)

Types define the format of a zettel's blob content, similar to file extensions. A zettel has at most one type. Types are referenced in queries with the ! prefix (e.g., !md:z matches all markdown zettels).

A zettel's type is supplied by the repo's default type when you omit one on new (or checkin). A standard init repo sets a default type (commonly !md). Workspace repos and clones have no default type, so new and checkin there require an explicit -type; omitting it errors with no type given and repo has no default type; pass -type. (Older data may also be typeless — it displays as a bare ! — and typeless objects break push/import, so always give a new zettel a type.) Set or change a workspace's default with init-workspace -type <type>.

Both tags and types can be viewed with dodder show :t (types) and dodder show :e (tags).

Dormant Objects

Dormant objects are hidden from default queries. Mark objects as dormant to archive or suppress them without deleting.

dodder dormant-add tag-name        # hide objects matching this tag
dodder dormant-remove tag-name     # unhide objects matching this tag
dodder dormant-edit                # open dormant configuration in editor

Dormant objects reappear in queries that use the ? sigil:

dodder show :?z                    # all zettels including dormant
dodder checkout :?z                # checkout including dormant

The dormant index is part of the repository configuration. Use dormant-edit to directly edit the configuration blob that controls which tags trigger dormancy.

Maintenance

dodder reindex                     # rebuild all indices from inventory lists
dodder fsck                        # verify integrity of objects and blobs
dodder fsck -skip-blobs            # skip blob content verification
dodder fsck -skip-probes           # skip probe index verification
dodder repo-fsck                   # verify repository-level integrity
dodder find-missing sha1 sha2      # check if blob SHAs exist in the store
dodder revert one/uno              # revert object to previous version
dodder revert -last                # revert all changes from last inventory list
dodder info store-version          # show current store version
dodder info compression-type       # show blob compression type
dodder info age-encryption         # show encryption status
dodder info env                    # show environment variables
dodder info xdg                    # show XDG directory paths
dodder deinit                      # remove dodder repository (requires confirmation)
dodder deinit -force               # remove without confirmation

reindex rebuilds the stream index and other derived data structures from the authoritative inventory lists. Run it after a suspected corruption or after manual edits to the store.

fsck verifies that every object's metadata, digest, and blob content are consistent. It reports errors but does not modify data.

Repository Initialization

dodder init my-repo                            # XDG-user repo named "my-repo"
dodder init .my-repo                           # create .dodder in current dir
dodder init -yin words.txt my-repo             # custom left-part word list
dodder init -yang words.txt my-repo            # custom right-part word list

The required positional is the new repo's location handle; its scope comes from the spelling. A handle that starts with . (e.g. .my-repo) creates a .dodder/ directory in the current working directory instead of using XDG base directories. This is useful for self-contained repositories. (-repo_id / DODDER_REPO_ID address an existing repo and are rejected on init / clone.)

Global Flags

These flags apply to all commands:

Flag	Purpose
-dir-dodder	Override the dodder directory path
-ignore-workspace	Ignore workspace defaults
-ignore-hook-errors	Continue despite hook failures
-hooks	Path to hooks configuration
-checkout-cache-enabled	Enable checkout caching
-predictable-zettel-ids	Generate IDs in order (testing)
-comment	Attach a comment to the inventory list
-debug	Enable debug output
-dry-run	Preview changes without applying
-verbose	Increase output verbosity

Reference Documents

• references/commands.md -- Complete command reference organized by workflow, with flags and one-line examples.
• references/querying.md -- Full query syntax reference with genres, sigils, filters, compound queries, and practical examples.