hypha CLI reference

The reference CMN client CLI — release spores, query synapses, resolve bonds, and manage your local mycelium.

hypha is compiled from a closed cli-spec-v1 registry: one source for argv parsing, typed invocation values, which parameter combinations are legal, output contracts, and help. An invocation runs only when it matches exactly one registered combination.

Global arguments

AFDATA registers these itself, so the syntax in Commands leaves them out.

Argument	Where	What it does
`--help`	every command	Every legal shape of that command, complete, plus its subcommands. JSON by default; `--output plain` for a terminal.
`--version`	hypha only	Name, version, and build identity as one protocol result.
`--docs`	hypha only	This document, rendered from the registry.
`--output <FORMAT>`	per output contract	Render as json, yaml, plain (default `json`).
`--output-to <DESTINATION>`	per output contract	Route results and diagnostics to split, stdout, stderr (default `split`).
`--stdout-file <PATH>`, `--stderr-file <PATH>`	per output contract	Append that stream to a file instead.

Success output is protocol events, on those terms, unless a command’s own Output line says otherwise.

A shape is one legal set of arguments that may appear together, under a stable id. Where a command has more than one, each id is a heading below. --help returns them all at once, so discovering a command costs one call; there is no recursive mode across commands, and this document is that view.

Commands

hypha absorb — Prepare spores for AI-assisted merge
hypha bond — Fetch bonds from spore.core.json
hypha cache clean — Remove old or all cached items
hypha cache list — List cached spores
hypha cache path — Show a cached spore’s filesystem path
hypha config list — Show merged Hypha configuration
hypha config set — Set one dotted configuration key
hypha grow — Update a spawned working copy through Synapse lineage
hypha hatch — Create or update spore.core.json
hypha hatch bond clear — Remove every bond
hypha hatch bond remove — Remove bonds matching a URI, relation, or both
hypha hatch bond set — Add or update one bond by URI
hypha hatch bond sync — Reconcile one relation to a declarative JSON spec
hypha hatch tree set — Set tree hashing configuration
hypha hatch tree show — Show tree hashing configuration
hypha lineage — Trace descendants or ancestors of a spore
hypha mycelium nutrient add — Add or update one nutrient method
hypha mycelium nutrient clear — Remove every nutrient method
hypha mycelium nutrient remove — Remove one nutrient method
hypha mycelium pulse — Send a signed mycelium to a Synapse
hypha mycelium root — Establish or update a domain site
hypha mycelium serve — Serve a local mycelium site over HTTP
hypha mycelium spore unyank — Restore a delisted spore from its retained manifest
hypha mycelium spore yank — Delist a spore while retaining published bytes
hypha mycelium status — Show local site status
hypha release — Sign and publish a spore
hypha replicate — Copy spores to another domain without changing hashes
hypha search — Search spores through a Synapse
hypha sense — Resolve a CMN URI and show its metadata
hypha skill install — Install or refresh the bundled skill
hypha skill status — Inspect whether the bundled skill is current
hypha skill uninstall — Remove the bundled skill
hypha spawn — Create a working copy of a spore
hypha synapse add — Add a Synapse node
hypha synapse config — Configure credentials for one Synapse
hypha synapse discover — Discover Synapse instances
hypha synapse health — Check one Synapse instance
hypha synapse list — List configured Synapse nodes
hypha synapse remove — Remove a Synapse node
hypha synapse use — Select the default Synapse node
hypha taste — Download a spore for review or record a verdict

`hypha absorb`

Prepare spores for AI-assisted merge

`absorb_explicit` — Absorb the listed URIs

hypha absorb [--log <CATEGORY>...] <CMN_URL>... [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>] [--max-depth <COUNT>]

`absorb_discover` — Discover descendants and absorb them

hypha absorb [--log <CATEGORY>...] --discover [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>] [--max-depth <COUNT>]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	One or more spore URIs
`--discover`	Discover descendants through Synapse
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token
`--max-depth`	Maximum lineage depth

`hypha bond`

Fetch bonds from spore.core.json

hypha bond [--log <CATEGORY>...] [--clean] [--status]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--clean`	Remove cached bonds no longer declared
`--status`	Show status without fetching

`hypha cache clean`

Remove old or all cached items

hypha cache clean [--log <CATEGORY>...] [--all]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--all`	Remove every cached item

`hypha cache list`

List cached spores

hypha cache list [--log <CATEGORY>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values

`hypha cache path`

Show a cached spore’s filesystem path

hypha cache path [--log <CATEGORY>...] <CMN_URL>

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	Spore URI

`hypha config list`

Show merged Hypha configuration

hypha config list [--log <CATEGORY>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values

`hypha config set`

Set one dotted configuration key

hypha config set [--log <CATEGORY>...] <KEY> <VALUE>

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`KEY`	Dotted configuration path
`VALUE`	Value to store

`hypha grow`

Update a spawned working copy through Synapse lineage

hypha grow [--log <CATEGORY>...] [--dist <archive|git>] [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>] [--bond]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--dist`	Override the distribution source
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token
`--bond`	Update and fetch bonds too

`hypha hatch`

Create or update spore.core.json

hypha hatch [--log <CATEGORY>...] [--id <ID>] [--version <VERSION>] [--name <NAME>] [--domain <DOMAIN>] [--synopsis <TEXT>] [--intent <TEXT>...] [--mutations <TEXT>...] [--license <SPDX>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--id`	Opaque spore identifier
`--version`	Spore version
`--name`	Display name
`--domain`	Publisher domain
`--synopsis`	Short description
`--intent`	Permanent intent; repeat for more entries
`--mutations`	Changes from the parent; repeat for more entries
`--license`	SPDX license identifier

`hypha hatch bond clear`

Remove every bond

hypha hatch bond clear [--log <CATEGORY>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values

`hypha hatch bond remove`

Remove bonds matching a URI, relation, or both

`hatch_bond_remove_uri` — Match by URI, optionally narrowed by relation

hypha hatch bond remove [--log <CATEGORY>...] --uri <CMN_URL> [--relation <RELATION>]

`hatch_bond_remove_relation` — Match every bond with one relation

hypha hatch bond remove [--log <CATEGORY>...] --relation <RELATION>

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--uri`	URI to match
`--relation`	Relation to match

`hypha hatch bond set`

Add or update one bond by URI

hypha hatch bond set [--log <CATEGORY>...] --uri <CMN_URL> [--relation <RELATION>] [--id <ID>] [--reason <TEXT>] [--with <KEY=VALUE>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--uri`	Bond URI and match key
`--relation`	Bond relation
`--id`	Bond id
`--reason`	Why this bond exists
`--with`	Bond parameter with a JSON value

`hypha hatch bond sync`

Reconcile one relation to a declarative JSON spec

hypha hatch bond sync [--log <CATEGORY>...] --relation <RELATION> --spec <PATH_OR_JSON> [--domain <DOMAIN>] [--site-path <PATH>] [--check]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--relation`	Relation to reconcile
`--spec`	JSON spec file, inline JSON, or stdin
`--domain`	Domain used to resolve omitted URIs
`--site-path`	Custom mycelium site directory
`--check`	Report drift without writing

`hypha hatch tree set`

Set tree hashing configuration

hypha hatch tree set [--log <CATEGORY>...] [--algorithm <ALGORITHM>] [--exclude-names <NAME>...] [--follow-rules <FILE>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--algorithm`	Tree hash algorithm
`--exclude-names`	File or directory name to exclude
`--follow-rules`	Ignore-rule file to follow

`hypha hatch tree show`

Show tree hashing configuration

hypha hatch tree show [--log <CATEGORY>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values

`hypha lineage`

Trace descendants or ancestors of a spore

hypha lineage [--log <CATEGORY>...] <CMN_URL> [--direction <in|out>] [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>] [--max-depth <COUNT>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	Spore URI
`--direction`	in for descendants, out for ancestors
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token
`--max-depth`	Maximum traversal depth

`hypha mycelium nutrient add`

Add or update one nutrient method

hypha mycelium nutrient add [--log <CATEGORY>...] <DOMAIN> --type <TYPE> [--with <KEY=VALUE>...] [--site-path <PATH>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Domain name
`--type`	Nutrient method type
`--with`	Nutrient parameter with a JSON value
`--site-path`	Custom mycelium site directory

`hypha mycelium nutrient clear`

Remove every nutrient method

hypha mycelium nutrient clear [--log <CATEGORY>...] <DOMAIN> [--site-path <PATH>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Domain name
`--site-path`	Custom mycelium site directory

`hypha mycelium nutrient remove`

Remove one nutrient method

hypha mycelium nutrient remove [--log <CATEGORY>...] <DOMAIN> --type <TYPE> [--site-path <PATH>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Domain name
`--type`	Nutrient method type
`--site-path`	Custom mycelium site directory

`hypha mycelium pulse`

Send a signed mycelium to a Synapse

hypha mycelium pulse [--log <CATEGORY>...] --file <PATH> [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--file`	Signed mycelium JSON file
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token

`hypha mycelium root`

Establish or update a domain site

`mycelium_root_domain` — Create or update an explicitly named domain

hypha mycelium root [--log <CATEGORY>...] <DOMAIN> [--site-path <PATH>] [--name <NAME>] [--synopsis <TEXT>] [--bio <MARKDOWN>] [--endpoints-base <URL>]

`mycelium_root_hub` — Create a taste-only identity under a hosted hub

hypha mycelium root [--log <CATEGORY>...] --hub <DOMAIN> [--site-path <PATH>] [--name <NAME>] [--synopsis <TEXT>] [--bio <MARKDOWN>]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Domain name
`--hub`	Hosted taste hub
`--site-path`	Custom mycelium site directory
`--name`	Site or author name
`--synopsis`	Brief site description
`--bio`	Site or author bio
`--endpoints-base`	Base URL for endpoints

`hypha mycelium serve`

Serve a local mycelium site over HTTP

hypha mycelium serve [--log <CATEGORY>...] [<DOMAIN>] [--site-path <PATH>] [--port <PORT>]

Output: protocol events; --output json/yaml/plain (default json), --output-to stdout/stderr (default stdout); redirect with --stdout-file or --stderr-file.

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Domain name
`--site-path`	Custom mycelium site directory
`--port`	TCP port

`hypha mycelium spore unyank`

Restore a delisted spore from its retained manifest

hypha mycelium spore unyank [--log <CATEGORY>...] --id <SPORE_ID> [--domain <DOMAIN>] [--site-path <PATH>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--id`	Spore id to restore
`--domain`	Domain used to locate the site
`--site-path`	Custom mycelium site directory

`hypha mycelium spore yank`

Delist a spore while retaining published bytes

hypha mycelium spore yank [--log <CATEGORY>...] --id <SPORE_ID> [--domain <DOMAIN>] [--site-path <PATH>] [--purge]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--id`	Spore id to delist
`--domain`	Domain used to locate the site
`--site-path`	Custom mycelium site directory
`--purge`	Delete the published manifest and archive too

`hypha mycelium status`

Show local site status

`mycelium_status_domain` — List sites or show one domain

hypha mycelium status [--log <CATEGORY>...] [<DOMAIN>] [--site-path <PATH>]

`mycelium_status_spore` — Resolve one spore id from one domain

hypha mycelium status [--log <CATEGORY>...] <DOMAIN> [--site-path <PATH>] --id <SPORE_ID>

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Domain name
`--site-path`	Custom mycelium site directory
`--id`	Resolve a spore from the inventory

`hypha release`

Sign and publish a spore

`release_archive` — Release from local source and archive

hypha release [--log <CATEGORY>...] --domain <DOMAIN> [--source <PATH>] [--site-path <PATH>] [--archive <zstd>] [--dry-run]

`release_git` — Release with an external git distribution

hypha release [--log <CATEGORY>...] --domain <DOMAIN> [--source <PATH>] [--site-path <PATH>] --dist-git <URL> --dist-ref <REF> [--archive <zstd>] [--dry-run]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--domain`	Target publisher domain
`--source`	Spore source directory
`--site-path`	Custom mycelium site directory
`--dist-git`	External git repository
`--dist-ref`	Tag, branch, or commit
`--archive`	Generated archive format
`--dry-run`	Compute the URI without writing

`hypha replicate`

Copy spores to another domain without changing hashes

`replicate_explicit` — Replicate the listed URIs

hypha replicate [--log <CATEGORY>...] <CMN_URL>... --domain <DOMAIN> [--site-path <PATH>]

`replicate_refs` — Replicate every declared non-self bond

hypha replicate [--log <CATEGORY>...] --refs --domain <DOMAIN> [--site-path <PATH>]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	One or more spore URIs
`--refs`	Replicate every non-self bond
`--domain`	Target publisher domain
`--site-path`	Custom mycelium site directory

`hypha search`

Search spores through a Synapse

hypha search [--log <CATEGORY>...] <QUERY> [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>] [--domain <DOMAIN>] [--license <SPDX>] [--bonds <RELATION:URI>] [--limit <COUNT>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`QUERY`	Search text
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token
`--domain`	Filter by publisher domain
`--license`	Filter by license
`--bonds`	Comma-separated bond filters
`--limit`	Maximum number of results

`hypha sense`

Resolve a CMN URI and show its metadata

hypha sense [--log <CATEGORY>...] <CMN_URL> [--id <SPORE_ID>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	CMN URI to resolve
`--id`	Resolve the latest spore with this id

`hypha skill install`

Install or refresh the bundled skill

`skill_install_standard` — Use the selected agent’s standard skills directory

hypha skill install [--log <CATEGORY>...] [--agent <all|codex|claude-code|opencode>] [--scope <personal|project>] [--force]

`skill_install_explicit_directory` — Use an explicit directory for one concrete agent

hypha skill install [--log <CATEGORY>...] --agent <codex|claude-code|opencode> [--scope <personal|project>] --skills-dir <PATH> [--force]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--agent`	Agent target
`--scope`	Install scope
`--skills-dir`	Explicit skills directory
`--force`	Replace an unmanaged target

`hypha skill status`

Inspect whether the bundled skill is current

`skill_status_standard` — Use the selected agent’s standard skills directory

hypha skill status [--log <CATEGORY>...] [--agent <all|codex|claude-code|opencode>] [--scope <personal|project>] [--force]

`skill_status_explicit_directory` — Use an explicit directory for one concrete agent

hypha skill status [--log <CATEGORY>...] --agent <codex|claude-code|opencode> [--scope <personal|project>] --skills-dir <PATH> [--force]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--agent`	Agent target
`--scope`	Install scope
`--skills-dir`	Explicit skills directory
`--force`	Replace an unmanaged target

`hypha skill uninstall`

Remove the bundled skill

`skill_uninstall_standard` — Use the selected agent’s standard skills directory

hypha skill uninstall [--log <CATEGORY>...] [--agent <all|codex|claude-code|opencode>] [--scope <personal|project>] [--force]

`skill_uninstall_explicit_directory` — Use an explicit directory for one concrete agent

hypha skill uninstall [--log <CATEGORY>...] --agent <codex|claude-code|opencode> [--scope <personal|project>] --skills-dir <PATH> [--force]

Arguments across every shape above:

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--agent`	Agent target
`--scope`	Install scope
`--skills-dir`	Explicit skills directory
`--force`	Replace an unmanaged target

`hypha spawn`

Create a working copy of a spore

hypha spawn [--log <CATEGORY>...] <CMN_URL> [<DIRECTORY>] [--vcs <git|none>] [--dist <archive|git>] [--bond]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	Spore URI to copy
`DIRECTORY`	Target directory
`--vcs`	Version-control initialization
`--dist`	Preferred distribution source
`--bond`	Fetch the spore’s bonds after spawning

`hypha synapse add`

Add a Synapse node

hypha synapse add [--log <CATEGORY>...] <URL>

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`URL`	Synapse URL

`hypha synapse config`

Configure credentials for one Synapse

hypha synapse config [--log <CATEGORY>...] <DOMAIN> [--token-secret <TOKEN>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Synapse domain
`--token-secret`	Token, or an empty string to clear

`hypha synapse discover`

Discover Synapse instances

hypha synapse discover [--log <CATEGORY>...] [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token

`hypha synapse health`

Check one Synapse instance

hypha synapse health [--log <CATEGORY>...] [<DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN_OR_URL`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token

`hypha synapse list`

List configured Synapse nodes

hypha synapse list [--log <CATEGORY>...]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values

`hypha synapse remove`

Remove a Synapse node

hypha synapse remove [--log <CATEGORY>...] <DOMAIN>

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Synapse domain

`hypha synapse use`

Select the default Synapse node

hypha synapse use [--log <CATEGORY>...] <DOMAIN>

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`DOMAIN`	Synapse domain

`hypha taste`

Download a spore for review or record a verdict

hypha taste [--log <CATEGORY>...] <CMN_URL> [--verdict <sweet|fresh|safe|rotten|toxic>] [--notes <TEXT>] [--synapse <DOMAIN_OR_URL>] [--synapse-token-secret <TOKEN>] [--domain <DOMAIN>]

Argument	Meaning
`--log`	Diagnostic category to emit; repeat or use comma-separated values
`CMN_URL`	CMN URI to evaluate
`--verdict`	Verdict to record
`--notes`	Notes accompanying the verdict
`--synapse`	Synapse domain or URL
`--synapse-token-secret`	Authentication token overriding the configured Synapse token
`--domain`	Domain used to sign a taste report

Exit codes

Code	Meaning
0	The command ran and succeeded.
1	The command ran and failed. The event carries a domain `error.code`.
2	The invocation was rejected before anything ran. `error.code` is one of the `cli_*` codes below.

The split is the useful one for a caller: exit 2 means the call was never made, so retrying it unchanged cannot help, while exit 1 means it was.

CLI errors

Every structural failure emits one strict JSON kind:"error" event on stderr, leaves stdout empty, and exits 2. The code names the failure — cli_unknown_argument for an unknown spelling, cli_unregistered_combination for registered arguments in a mixture that is not, and one each for cli_unknown_command, cli_missing_argument_value, cli_invalid_argument_value, cli_duplicate_argument, cli_unexpected_positional, and cli_invalid_utf8. message identifies a safe argument spelling or the failure category and hint gives the command to run next; neither ever quotes a raw value, including secrets. These are decided before any config, secret source, filesystem, network, or domain I/O.

Two exit-1 codes describe the tool itself rather than the call: cli_invocation_invalid means the program misread its own resolved invocation — an unknown action id, or an argument id the selected combination cannot produce — and output_setup_failed means an output sink (--stdout-file, --stderr-file, stream redirection) could not be established. Both are defects to report, not inputs to correct; retrying the same command cannot help.

Domain failures (exit 1) carry their own stable error.code instead, drawn from whatever this tool defines rather than from the cli_* set. No error message quotes a raw value it was given — an error event is routinely logged, and the input may hold secrets.

Global arguments

Commands

hypha absorb

absorb_explicit — Absorb the listed URIs

absorb_discover — Discover descendants and absorb them

hypha bond

hypha cache clean

hypha cache list

hypha cache path

hypha config list

hypha config set

hypha grow

hypha hatch

hypha hatch bond clear

hypha hatch bond remove

hatch_bond_remove_uri — Match by URI, optionally narrowed by relation

hatch_bond_remove_relation — Match every bond with one relation

hypha hatch bond set

hypha hatch bond sync

hypha hatch tree set

hypha hatch tree show

hypha lineage

hypha mycelium nutrient add

hypha mycelium nutrient clear

hypha mycelium nutrient remove

hypha mycelium pulse

hypha mycelium root

mycelium_root_domain — Create or update an explicitly named domain

mycelium_root_hub — Create a taste-only identity under a hosted hub

hypha mycelium serve

hypha mycelium spore unyank

hypha mycelium spore yank

hypha mycelium status

mycelium_status_domain — List sites or show one domain

mycelium_status_spore — Resolve one spore id from one domain

hypha release

release_archive — Release from local source and archive

release_git — Release with an external git distribution

hypha replicate

replicate_explicit — Replicate the listed URIs

replicate_refs — Replicate every declared non-self bond

hypha search

hypha sense

hypha skill install

skill_install_standard — Use the selected agent’s standard skills directory

skill_install_explicit_directory — Use an explicit directory for one concrete agent

hypha skill status

skill_status_standard — Use the selected agent’s standard skills directory

skill_status_explicit_directory — Use an explicit directory for one concrete agent

hypha skill uninstall

skill_uninstall_standard — Use the selected agent’s standard skills directory

skill_uninstall_explicit_directory — Use an explicit directory for one concrete agent

hypha spawn

hypha synapse add

hypha synapse config

hypha synapse discover

hypha synapse health

hypha synapse list

hypha synapse remove

hypha synapse use

hypha taste

Exit codes

CLI errors

`hypha absorb`

`absorb_explicit` — Absorb the listed URIs

`absorb_discover` — Discover descendants and absorb them

`hypha bond`

`hypha cache clean`

`hypha cache list`

`hypha cache path`

`hypha config list`

`hypha config set`

`hypha grow`

`hypha hatch`

`hypha hatch bond clear`

`hypha hatch bond remove`

`hatch_bond_remove_uri` — Match by URI, optionally narrowed by relation

`hatch_bond_remove_relation` — Match every bond with one relation

`hypha hatch bond set`

`hypha hatch bond sync`

`hypha hatch tree set`

`hypha hatch tree show`

`hypha lineage`

`hypha mycelium nutrient add`

`hypha mycelium nutrient clear`

`hypha mycelium nutrient remove`

`hypha mycelium pulse`

`hypha mycelium root`

`mycelium_root_domain` — Create or update an explicitly named domain

`mycelium_root_hub` — Create a taste-only identity under a hosted hub

`hypha mycelium serve`

`hypha mycelium spore unyank`

`hypha mycelium spore yank`

`hypha mycelium status`

`mycelium_status_domain` — List sites or show one domain

`mycelium_status_spore` — Resolve one spore id from one domain

`hypha release`

`release_archive` — Release from local source and archive

`release_git` — Release with an external git distribution

`hypha replicate`

`replicate_explicit` — Replicate the listed URIs

`replicate_refs` — Replicate every declared non-self bond

`hypha search`

`hypha sense`

`hypha skill install`

`skill_install_standard` — Use the selected agent’s standard skills directory

`skill_install_explicit_directory` — Use an explicit directory for one concrete agent

`hypha skill status`

`skill_status_standard` — Use the selected agent’s standard skills directory

`skill_status_explicit_directory` — Use an explicit directory for one concrete agent

`hypha skill uninstall`

`skill_uninstall_standard` — Use the selected agent’s standard skills directory

`skill_uninstall_explicit_directory` — Use an explicit directory for one concrete agent

`hypha spawn`

`hypha synapse add`

`hypha synapse config`

`hypha synapse discover`

`hypha synapse health`

`hypha synapse list`

`hypha synapse remove`

`hypha synapse use`

`hypha taste`