@fnndsc/brasa 0.33.4 → 0.35.0

package/dist/builtins/help.js

@@ -8,36 +8,12 @@
 import { gamesShelf_render, gamesShelf_names } from './games/shelf.js';
 import chalk from 'chalk';
 import { CAT_USAGE } from './fs/cat.args.js';
-/**
- * Standard subcommands and options injected into every resource help entry.
- * Captures the Resource Contract documented in CONTEXT.md.
- */
-export const RESOURCE_LIST_OPTIONS = [
-    '',
-    'STANDARD SUBCOMMANDS:',
-    '  list              List resources (default: 20 per page)',
-    '  search <term>     Search resources (alias: list --search <term>)',
-    '  inspect           List available field names',
-    '',
-    'STANDARD OPTIONS:',
-    '  --all             Fetch all pages',
-    '  --limit <n>       Page size (default: 20)',
-    '  --fields <f,f>    Columns to display',
-    '  --sort <field>    Sort by field',
-    '  --reverse         Reverse sort order',
-    '  --table           Tabular output',
-    '  --csv             CSV output',
-];
+import { commands_register, commandHelpEntry_get, helpTopic_names, builtinCommand_has } from '../core/commandRegistry.js';
+import { backendInstalled_get } from '../core/backend.js';
 /**
  * Help-text registry keyed by builtin command name.
  */
 export const helpText = {
-    user: {
-        usage: 'user <add|inspect|disable|enable|remove> <username>',
-        description: 'Manage CUBE-local accounts; federated identities remain externally managed',
-        options: ['Use `sudo user …` for lifecycle operations.', 'add prompts for email and a hidden password confirmation.'],
-        examples: ['sudo user add jack.bivowac', 'sudo user disable jack.bivowac', 'sudo user remove jack.bivowac'],
-    },
     sudo: {
         usage: 'sudo <command> [arguments...]',
         description: 'Run one ChRIS command with a temporary administrator identity',
@@ -87,19 +63,6 @@ export const helpText = {
             'cd                    # Show current directory',
         ],
     },
-    netstat: {
-        usage: 'netstat [-n <count>] [-r]',
-        description: 'What the session has asked of CUBE: requests since the session (or the last reset), by endpoint family with the time spent, and the last few timed',
-        options: [
-            '-n <count>   List that many recent requests (default 10)',
-            '-r, --reset  Forget the count after showing it',
-        ],
-        examples: [
-            'netstat              # the count, by family, the last 10',
-            'netstat -n 30        # the last 30 requests, timed',
-            'netstat -r; cd ~/feeds; netstat   # what one navigation costs',
-        ],
-    },
     pwd: {
         usage: 'pwd [options]',
         description: 'Print current working directory',
@@ -135,93 +98,6 @@ export const helpText = {
             'cat file1 file2                 # Display multiple files',
         ],
     },
-    edit: {
-        usage: 'edit <file>',
-        description: 'Edit a ChRIS file in $EDITOR — fetches, opens, saves back on write',
-        options: [
-            'Uses $EDITOR (or $VISUAL, or vi as fallback)',
-            'No-ops if file is unchanged on exit',
-            'On save: deletes original and re-uploads — file path preserved, ID changes',
-            'On upload failure: edited content preserved in /tmp',
-        ],
-        examples: [
-            'edit /home/chris/uploads/config.yaml',
-            'edit notes.txt',
-            'EDITOR=nano edit report.json',
-        ],
-    },
-    setfacl: {
-        usage: 'setfacl -m u:<user>:r|g:<group>:r|o::r|o::- <path>... | setfacl -x u:<user>|g:<group> <path>...',
-        summary: 'Share a feed with a user, a group or everyone, or stop sharing it',
-        description: 'A feed\'s access list, as POSIX ACL entries. -m u:<user>:r shares it with a user, -m g:<group>:r '
-            + 'with a group, -m o::r with everyone (a public feed) and -m o::- makes it private again. '
-            + '-x u:<user> or -x g:<group> withdraws that grant. A feed is named by id, by the feed_N a '
-            + 'listing shows, by any path through /feeds/, or by /proc/jobs/feed_N. Given a feed and no '
-            + 'entry, it asks which user to share it with.',
-        options: [
-            '-m u:<user>:r     Share with a user (the perms must include r)',
-            '-m g:<group>:r    Share with a group',
-            '-m o::r | o::-    Make the feed public, or private again (chmod o+r / o-r is the same)',
-            '-x u:<user>       Stop sharing with a user',
-            '-x g:<group>      Stop sharing with a group',
-        ],
-        examples: [
-            'setfacl -m u:someone:r /home/me/feeds/feed_12',
-            'setfacl -m g:grantlab:r feed_12 feed_13',
-            'setfacl -m o::r feed_12                  # public',
-            'setfacl -x u:someone feed_12',
-            'setfacl feed_12                          # asks who to share it with',
-        ],
-    },
-    getfacl: {
-        usage: 'getfacl <path>...',
-        summary: 'Show who can read a feed: users, groups, and whether it is public',
-        description: 'Show who can read a feed, in the familiar block: a # file: line, the owner\'s user:: entry, '
-            + 'one user: line per user and one group: line per group holding access, then other:: '
-            + '(r-- when the feed is public).',
-        examples: [
-            'getfacl /home/me/feeds/feed_12',
-        ],
-    },
-    chmod: {
-        usage: 'chmod o+r|o-r <feed>...',
-        summary: 'Make a feed public, or private again',
-        description: 'The other entry of a feed\'s access list spelled as a mode: o+r makes it public, o-r private, '
-            + 'exactly as setfacl -m o::r and o::- do. No other mode is one a feed has.',
-        examples: [
-            'chmod o+r feed_12',
-            'chmod o-r /proc/jobs/feed_12',
-        ],
-    },
-    setfattr: {
-        usage: 'setfattr -n tag -v <value> <path>... | setfattr -x tag [-v <value>] <path>...',
-        summary: 'Hang a tag on a feed, or take it off',
-        description: 'A feed\'s tags are the values of one extended attribute, tag (also user.tag): CUBE\'s '
-            + 'freeform labels. -n tag -v <value> hangs one of your tags (a folder under /proc/tags: '
-            + 'mkdir /proc/tags/<name> makes a tag, and naming one that does not exist is an error); '
-            + '-x tag -v <value> takes it off; -x tag alone takes every tag off, as '
-            + 'setfattr removes the whole attribute. A feed is named by id, by feed_N, by any path '
-            + 'through /feeds/, or by its projection /proc/jobs/feed_N. Silent on success.',
-        options: [
-            '-n, --name tag        The attribute to set (only tag exists)',
-            '-v, --value <value>   The tag',
-            '-x, --remove tag      Remove the tag given by -v, or every tag without -v',
-        ],
-        examples: [
-            'setfattr -n tag -v urgent feed_12',
-            'setfattr -n tag -v review feed_12 feed_13',
-            'setfattr -x tag -v urgent /proc/jobs/feed_12',
-        ],
-    },
-    getfattr: {
-        usage: 'getfattr [-n tag] <path>...',
-        summary: 'Show the tags a feed wears',
-        description: 'Show a feed\'s tags in getfattr\'s dump shape: a # file: line, then one tag="…" line per tag.',
-        examples: [
-            'getfattr feed_12',
-            'getfattr -n tag /home/me/feeds/feed_12',
-        ],
-    },
     rm: {
         usage: 'rm [options] <path> [path...]',
         description: 'Remove files or directories',
@@ -298,15 +174,6 @@ export const helpText = {
             'touch --withContentsFromFile template.json config.json  # Create from local file',
         ],
     },
-    config: {
-        usage: 'config write <cfs-path> <base64-content>',
-        description: 'Write a small configuration document into the user\'s CUBE home (the durable layer: argus desktops, surface preferences). Reads travel the ordinary cat. Documents are notes, not datasets: 256KB limit.',
-        options: [],
-        examples: [
-            'config write ~/.config/argus/desktops/quad.desk dmlldyBmaWxlcwo=   # a saved argus desktop',
-            'cat ~/.config/argus/desktops/quad.desk                             # reading one back',
-        ],
-    },
     mkdir: {
         usage: 'mkdir [-p] <directory> [directory...]',
         description: 'Create directories',
@@ -331,482 +198,16 @@ export const helpText = {
             'rmdir /proc/tags/old       # Delete a tag no feed wears',
         ],
     },
-    upload: {
-        usage: 'upload <local_path_or_glob> <chris_path>',
-        description: 'Upload local files, directories, or glob matches to ChRIS with progress tracking',
-        options: [
-            'Displays progress bar showing:',
-            '  - File count and percentage complete',
-            '  - Estimated time remaining (ETA)',
-            '  - Data transfer progress',
-            'Shows summary statistics after upload',
-        ],
-        examples: [
-            'upload ~/data/file.csv /home/user/uploads/',
-            'upload ~/Pictures/earthandmoon* .',
-            'upload ./results/ ~/data/',
-            'upload ~/experiment/data /home/user/projects/',
-        ],
-    },
-    download: {
-        usage: 'download <chris_path_or_glob> <local_path> [-f|--force]',
-        description: 'Download a ChRIS file, directory, or CFS glob to the local filesystem with progress tracking',
-        options: [
-            '-f, --force   Overwrite existing local paths',
-            'Progress bar shows files, ETA, bytes transferred',
-        ],
-        examples: [
-            'download /home/user/data ./data',
-            'download /home/user/results/*.nii ./results/',
-            'download /feeds/feed_123 ./downloads -f',
-        ],
-    },
-    connect: {
-        usage: 'connect <username> <url> [password]',
-        description: 'Connect to ChRIS server',
-        examples: [
-            'connect alice https://cube.chrisproject.org/api/v1/',
-            'connect bob http://localhost:8000/api/v1/ mypassword',
-        ],
-    },
-    logout: {
-        usage: 'logout',
-        description: 'Disconnect from ChRIS server',
-        examples: ['logout'],
-    },
-    plugin: {
-        usage: 'plugin <subcommand> [options]',
-        description: 'Work with a single ChRIS plugin - run, search, view documentation',
-        options: [
-            '',
-            'DESCRIPTION:',
-            '  Plugins are computational units in ChRIS that process data. The "plugin"',
-            '  command operates on individual plugins - running them, searching for specific',
-            '  plugins, or viewing their documentation.',
-            '',
-            'SUBCOMMANDS:',
-            '  run [--detach] <searchable> [params]  Run a plugin and wait for it to finish',
-            '                               (--detach returns the instance id at once)',
-            '  info <name>-v<version>       Show one plugin whole: facts and every parameter',
-            '  search <searchable>          Resolve a searchable to plugin IDs',
-            '  readme <pluginId>            Display plugin README documentation',
-            '',
-            'SEARCHABLE FORMATS:',
-            '  Simple:     pl-dircopy',
-            '  Compound:   name:pl-dircopy,version:1.3.2',
-            '  ID-based:   id:42',
-            '  Batch:      id:77++id:33  (multiple plugins)',
-            '',
-            'PLUGIN RUN PARAMETERS:',
-            '  Plugin-specific parameters use CLI flag format:',
-            '    --param value              Single parameter',
-            '    --flag                     Boolean flag',
-            '    --param1 val1 --param2 val2   Multiple parameters',
-            '',
-            '  Run "parametersofplugin <name>" to see available parameters for a plugin.',
-        ],
-        examples: [
-            '# Read one plugin: the same manual "cat /bin/<entry>" prints',
-            'plugin info pl-dircopy-v1.0.0',
-            'plugin info pl-dircopy 1.0.0',
-            '',
-            '# Search for plugins',
-            'plugin search pl-dircopy',
-            'plugin search name:dcm2niix',
-            'plugin search id:42',
-            '',
-            '# View plugin documentation',
-            'plugin readme 42',
-            'plugin readme pl-dircopy',
-            '',
-            '# Run a plugin (simple)',
-            'plugin run pl-dircopy',
-            '',
-            '# Run plugin with parameters',
-            'plugin run pl-dircopy --dir /incoming',
-            'plugin run name:pl-dcm2niix,version:1.0.2 --outputdir /results',
-            '',
-            '# Run with multiple parameters',
-            'plugin run pl-segmentation --threshold 0.5 --method watershed',
-            '',
-            '# Run with specific version',
-            'plugin run name:pl-dircopy,version:2.1.1 --dir /data',
-        ],
-    },
-    plugins: {
-        usage: 'plugins <subcommand> [options]',
-        description: 'Manage collections of ChRIS plugins - list, add, delete, query',
-        options: [
-            '',
-            'DESCRIPTION:',
-            '  Plugins are computational units in ChRIS. The "plugins" command operates on',
-            '  collections of plugins - listing all available plugins, adding new plugins to',
-            '  ChRIS, deleting plugins, or querying plugin metadata.',
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  add <input>       [admin] Register a new plugin to ChRIS',
-            '  delete <id>       [admin] Remove a plugin from ChRIS',
-            '  overview          Show plugin system overview',
-            '',
-            'PLUGINS ADD OPTIONS:',
-            '  --compute <resources>         Comma-separated compute resources (default: host)',
-            '  --store <url>                 Peer store URL (default: cube.chrisproject.org)',
-            '  --adminUser <username>        Administrator username (non-interactive compatibility)',
-            '  --adminPassword <password>    Administrator password (non-interactive compatibility)',
-            '  --publicRepo <url>            Public repository URL for the plugin',
-            '',
-            'PLUGIN INPUT FORMATS:',
-            '  Plugin name:      pl-dircopy',
-            '  Docker image:     fnndsc/pl-dircopy:2.1.1',
-            '  Store URL:        https://cube.chrisproject.org/api/v1/plugins/96/',
-        ],
-        examples: [
-            '# List all plugins',
-            'plugins list',
-            'plugins list --all',
-            'plugins list --search name:dircopy',
-            'plugins list --fields name,version,dock_image',
-            'plugins search dircopy',
-            '',
-            '# Inspect available fields',
-            'plugins inspect',
-            '',
-            '# Delete a plugin',
-            'plugins delete 42',
-            '',
-            '# Show plugin system overview',
-            'plugins overview',
-            '',
-            '# Add plugin from peer store (searches cube.chrisproject.org)',
-            'plugins add pl-dircopy',
-            'plugins add pl-dircopy --compute host,gpu',
-            '',
-            '# Add a plugin with a temporary administrator identity',
-            'sudo plugins add pl-dircopy',
-            '',
-            '# Add plugin from Docker image',
-            'plugins add fnndsc/pl-dircopy:2.1.1',
-            'plugins add fnndsc/pl-dircopy:2.1.1 --compute host',
-            '',
-            '# Add plugin from custom peer store',
-            'plugins add pl-custom --store https://my-cube.org/api/v1/',
-            '',
-            '# Add plugin with specific repository',
-            'plugins add my-plugin:latest --publicRepo https://github.com/org/my-plugin',
-        ],
-    },
-    feed: {
-        usage: 'feed <subcommand> [options]',
-        description: 'Work with a single ChRIS feed - create, annotate, comment',
-        options: [
-            '',
-            'SUBCOMMANDS:',
-            '  create <path>                    Create a new feed from a data directory',
-            '  note <feedId>                    Show the feed\'s note',
-            '  note edit <feedId>               Edit the note in the surface\'s editor (edit /proc/jobs/feed_N/note)',
-            '  note <feedId> --title <t>        Update note title',
-            '  note <feedId> --content <c>      Update note content',
-            '  comments <feedId>                List all comments on a feed',
-            '  comment add <feedId>             Add a comment (--title, --content)',
-            '  comment edit <feedId> <commentId>  Edit a comment (--title, --content)',
-            '  comment delete <feedId> <commentId>  Delete a comment',
-            '  rm [<feed>] [-f]                 Remove a feed and everything in it (asks first)',
-            '  tree [<feed>]                     Render the feed\'s plugin-instance DAG',
-            '  tree [<feed>] --focus <id>        Scope the tree to one node\'s subtree',
-            '  tree [<feed>] --max-nodes <n>     Cap rendered nodes (0 = all)',
-            '  diagram [<feed>]                  Shallow alias of feed tree',
-            '  diagram --signalflow [<feed>]     Emit the DAG as SignalFlow YAML to stdout',
-            '                                   (pipe it: feed diagram --signalflow 42 | signalflow -)',
-            '',
-            '  <feed> accepts an ID, feed_N directory name, exact title, or unique search.',
-            '  Omit it while inside a feed_N path to use the current directory\'s feed.',
-        ],
-        examples: [
-            'feed create /home/user/uploads/MRI-data',
-            'feed tree 1669',
-            'feed diagram                       # Current feed, from inside feed_N',
-            'feed note 42',
-            'feed note 42 --title "QC passed" --content "No artefacts found"',
-            'feed comments 42',
-            'feed comment add 42 --title "Issue" --content "Slice 14 looks odd"',
-            'feed comment edit 42 7 --content "Resolved — motion artefact, excluded"',
-            'feed comment delete 42 7',
-        ],
-    },
-    feeds: {
-        usage: 'feeds <subcommand> [options]',
-        description: 'Manage collections of ChRIS feeds - list, delete, share, query',
-        options: [
-            '',
-            'DESCRIPTION:',
-            '  A feed represents a data analysis workflow in ChRIS - a DAG of linked plugin',
-            '  instances, also navigable as a folder at /home/<user>/feeds/.',
-            ...RESOURCE_LIST_OPTIONS,
-            '--user <username>   Filter by owner username (admin only)',
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  delete <id>       Remove a feed',
-        ],
-        examples: [
-            'feeds list',
-            'feeds list --all',
-            'feeds list --limit 100',
-            'feeds search experiment',
-            'feeds list --fields id,name,creation_date',
-            'feeds list --user radstar',
-            'feeds list --all --user radstar',
-            'feeds inspect',
-            'feeds delete 123',
-        ],
-    },
-    files: {
-        usage: 'files <subcommand> [path] [options]',
-        description: 'Manage ChRIS file resources',
-        options: [...RESOURCE_LIST_OPTIONS],
-        examples: [
-            'files list',
-            'files list /path',
-            'files search fname:dicom',
-            'files inspect',
-        ],
-    },
-    links: {
-        usage: 'links <subcommand> [path] [options]',
-        description: 'Manage ChRIS link resources',
-        options: [...RESOURCE_LIST_OPTIONS],
-        examples: ['links list', 'links search', 'links inspect'],
-    },
-    dirs: {
-        usage: 'dirs <subcommand> [path] [options]',
-        description: 'Manage ChRIS directory resources',
-        options: [...RESOURCE_LIST_OPTIONS],
-        examples: ['dirs list', 'dirs search', 'dirs inspect'],
-    },
-    pipeline: {
-        usage: 'pipeline <subcommand> [args]',
-        description: 'Manage and execute ChRIS pipelines (registered DAG workflows)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  info <name|id>        Show pipeline nodes, plugins, and topology',
-            '  manifest <name|id|slug>  Emit complete registered invocation YAML',
-            '  run <name|id>         Run a pipeline on the context node and wait for it',
-            '  source <name|id>      Display the pipeline YAML source file',
-            '  diagram <name|id>     Draw the pipeline as a shallow tree',
-            '    --withargs          Include stored non-null plugin defaults inline',
-            '    --signalflow        Emit SignalFlow YAML instead of the shallow tree',
-            '  delete <id>           Remove a pipeline',
-            '',
-            'RUN OPTIONS:',
-            '  --detach              Return the instance ids at once, without waiting',
-            '  --compute <resource>  Override compute resource for all nodes',
-            '  --previous <inst_id>  Explicit previous instance ID (default: context node)',
-            '  --paramFile <cfs-file> Apply one sparse YAML invocation overlay',
-            '  --<node>.<parameter> <value>  Override one hosted plugin parameter',
-            '  --<node>.<control> <value>    Override one node execution control',
-            '  Use --@<piping-id>.<field> when a node title is ambiguous or shell-unsafe',
-            '',
-            'PIPELINE EXECUTABLES:',
-            '  Pipelines also appear in /bin (colored magenta) and can be invoked directly.',
-            '  <PipelineName>              Run pipeline on context node',
-            '  <PipelineName> --nodes      Show DAG structure (alias: --parameters)',
-            '  <PipelineName> --source     Show YAML source (alias: --readme)',
-            '  <PipelineName> --manifest   Emit complete registered invocation YAML',
-            '  <PipelineName> --diagram    Draw the shallow pipeline topology',
-            '  <PipelineName> --signalflow Emit SignalFlow YAML directly',
-            '    --withargs                Include arguments with --diagram',
-            '  cat /bin/<PipelineName>     Show a fast cached executable summary',
-        ],
-        examples: [
-            'pipeline list                          # List all pipelines',
-            'pipeline list PHI                      # Filter by name',
-            'pipeline info PHI_detection            # Show nodes and topology',
-            'pipeline manifest PHI_detection        # Registered invocation YAML',
-            'pipeline run PHI_detection             # Run on current context node',
-            'pipeline run PHI_detection --compute gpu',
-            'pipeline run PHI_detection --segmentation.threshold 0.5',
-            'pipeline run PHI_detection --paramFile ~/params/run.yaml',
-            'pipeline source PHI_detection          # Show YAML source',
-            'pipeline diagram PHI_detection         # Draw the authored DAG',
-            'pipeline diagram --withargs PHI_detection',
-            'pipeline diagram --signalflow PHI_detection | signalflow -',
-            '',
-            '# Direct invocation from /bin',
-            'PHI_detection                          # Run with defaults',
-            'PHI_detection --nodes                  # Show node structure',
-            'PHI_detection --source                 # Show YAML source',
-            'PHI_detection --manifest               # Registered invocation YAML',
-            'PHI_detection --diagram                # Draw the authored DAG',
-            'PHI_detection --signalflow             # Emit SignalFlow YAML',
-            'cat /bin/PHI_detection                 # Cached executable summary',
-        ],
-    },
-    pacs: {
-        usage: 'pacs <subcommand> [args]',
-        description: 'PACS subsystem — server context, query, and series retrieval',
-        options: [
-            'SUBCOMMANDS:',
-            '  connect               List registered PACS servers with active one marked',
-            '  connect <name|id>     Set active PACS server',
-            '  disconnect            Clear active PACS server',
-            '  list                  List registered PACS servers (alias: pacs connect)',
-            '  query <Key:Value...>  Create PACS query and wait for results',
-            '  pull <vfs-path...>    Pull DICOM series into ChRIS storage',
-            '  status <target>       Per-series pulled/pending report with in-CUBE paths;',
-            '                        target is an expression, VFS path, or query id',
-        ],
-        examples: [
-            'pacs                              # Show active server',
-            'pacs connect                      # List all servers',
-            'pacs connect PACSDCM              # Set active server by identifier',
-            'pacs connect 1                    # Set active server by numeric ID',
-            'pacs disconnect                   # Clear active server',
-            'pacs list                         # List all servers',
-            'pacs query PatientID:1234         # Query PACS',
-            'pacs pull /net/pacs/queries/42_AccessionNumber:12345678',
-            'pacs status AccessionNumber:22119730   # What has landed in CUBE, what is missing',
-        ],
-    },
-    'pacs query': {
-        usage: 'pacs query <Key:Value[,Key:Value...]> [--table | --csv | --csv-to <cfs-path>] [--series] [--title <title>] [--pacsserver <id>] [--fresh]',
-        description: 'Create a PACS query, wait for results, and print the VFS path',
-        options: [
-            '--title <title>      Title for the query record (default: Query <timestamp>)',
-            '--pacsserver <id>    Override PACS server (default: context PACSserver);',
-            '                     a comma-separated list asks each and names the server on every row',
-            '--patients <list>    Ask after several patients: MRNs comma-separated, or @<cfs-file>',
-            '                     (one MRN per line; blanks and # comments ignored)',
-            '--csv                Render the answer as CSV (a row per study, and one per patient with none)',
-            '--csv-to <cfs-path>  Write that CSV into ChRIS storage, where a detached surface can reach it',
-            '                     (given no path, the destination is asked for)',
-            '--force              Overwrite the table at that path; without it, an existing file is kept',
-            '--table              Show the answer\'s rows as an aligned table: the CSV\'s columns, for a screen',
-            '--series             One row per series instead of per study (on the table and in the CSV);',
-            '                     alone, it shows the series table',
-            '--anon               Stand in for names and record numbers (for demonstrating on a live PACS)',
-            '--fresh              Ask the PACS even if this question was answered before',
-            '--help               Show this help',
-        ],
-        examples: [
-            'pacs query PatientID:1234',
-            'pacs query PatientID:1234 --fresh      # ignore the stored answer',
-            'pacs query AccessionNumber:12345678 --title "Hip DDH workup"',
-            'pacs query PatientID:1234,StudyDate:20240101',
-            'pacs query PatientID:1234 --table      # the rows, aligned, one per study',
-            'pacs query PatientID:1234 --series     # one row per series',
-            'pacs query PatientID:1234 --csv-to ~/audit.csv --table --series',
-            '',
-            '# Standalone alias (identical behaviour)',
-            'query PatientID:1234',
-        ],
-    },
-    'pacs pull': {
-        usage: 'pacs pull [--nowait] [--retry N] [--new-feed <title> [--plugin <selector>|--pipeline <selector>] [-- <args...>]] <vfs-path|query-expr> [...]',
-        description: 'Pull PACS series into ChRIS storage (blocking, with LONK progress)',
-        options: [
-            '--detach      Fire retrieves and return the handles at once; prints <seriesUID> <retrieveId> per line',
-            '              (--nowait is the older spelling of the same flag)',
-            '--retry N     Re-fire retrieves for [NO LONK] series up to N additional times',
-            '--new-feed <title>  Create one named feed from the complete retrieved selection',
-            '--plugin <selector> Attach one plugin to the new Feed root',
-            '--pipeline <selector> Attach one pipeline to the new Feed root',
-            '-- <args...>        Forward remaining tokens to the selected analysis',
-            '                    (cannot be combined with --detach)',
-            '--help        Show this help',
-        ],
-        examples: [
-            'pacs pull /net/pacs/queries/42_AccessionNumber:12345678',
-            'pacs pull /net/pacs/queries/42_.../Study_1.2.3_US-Hips_DDH',
-            'pacs pull AccessionNumber:12345678   # query-then-pull shorthand',
-            'pacs pull AccessionNumber:12345678 --new-feed "Brain MRI"',
-            '',
-            '# Standalone alias (identical behaviour)',
-            'pull /net/pacs/queries/42_AccessionNumber:12345678',
-        ],
-    },
-    'pacs connect': {
-        usage: 'pacs connect [<name|id>]',
-        description: 'List registered PACS servers or set the active one',
-        examples: [
-            'pacs connect                  # List all servers with active marked',
-            'pacs connect PACSDCM          # Set active server by identifier',
-            'pacs connect 1                # Set active server by numeric ID',
-        ],
-    },
-    'pacs disconnect': {
-        usage: 'pacs disconnect',
-        description: 'Clear the active PACS server from context',
-        examples: [
-            'pacs disconnect               # Clear active server',
-        ],
-    },
-    'pacs list': {
-        usage: 'pacs list',
-        description: 'List registered PACS servers with active one marked (alias: pacs connect)',
-        examples: [
-            'pacs list                     # List all servers',
-        ],
-    },
-    pacsservers: {
-        usage: 'pacsservers <subcommand> [options]',
-        description: 'List or inspect available PACS servers (context-aware)',
-        examples: [
-            'pacsservers list         # List PACS servers',
-            'pacsservers list --table # Table view',
-            'pacsservers fieldslist   # Show fields',
-        ],
-    },
-    pacsqueries: {
-        usage: 'pacsqueries <subcommand> [options]',
-        description: 'Create or list PACS queries (uses current pacsserver context unless overridden)',
-        options: [
-            '--pacsserver <id|name>  Use specific PACS server for this call',
-            '--title <string>        Title for created query',
-            '--search <filters>      Filters for list (supports comma-separated key:value)',
-        ],
-        examples: [
-            'pacsqueries list                          # List for current pacsserver',
-            'pacsqueries list --pacsserver PACSDCM     # Override server',
-            'pacsqueries create "PatientID:1234" --title "PID 1234"',
-            'pacsqueries decode <id>                   # Decode a query result',
-        ],
-    },
-    pacsretrieve: {
-        usage: 'pacsretrieve <subcommand> [options]',
-        description: 'Pull or inspect DICOM retrieves for PACS queries',
-        examples: [
-            'pacsretrieve pull <queryId>       # Pull data for a query',
-            'pacsretrieve report <queryId>     # Show retrieve status',
-            'pacsretrieve cancel <retrieveId> # Cancel a retrieve',
-        ],
-    },
     exit: {
         usage: 'exit',
         description: 'Exit the shell',
         examples: ['exit'],
     },
-    context: {
-        usage: 'context',
-        description: 'Display current ChRIS context information',
-        examples: ['context'],
-    },
-    whoami: {
-        usage: 'whoami',
-        description: 'Print the currently authenticated ChRIS username',
-        examples: ['whoami'],
-    },
     version: {
         usage: 'version',
         description: 'Report the versions of the mise stack layers running this session',
         examples: ['version'],
     },
-    id: {
-        usage: 'id',
-        description: 'Print the current CUBE user as a Unix-style UID, projected primary GID, and complete list of CUBE group memberships.',
-        examples: ['id'],
-    },
     fortune: {
         usage: 'fortune',
         summary: 'Print a random fortune cookie',
@@ -931,19 +332,6 @@ export const helpText = {
         description: 'The time, how long the process serving this session has run, how many surfaces are attached, since when, and its pid.',
         examples: ['uptime'],
     },
-    ping: {
-        usage: 'ping [-c N] [cube]',
-        summary: 'Round trips to CUBE, timed',
-        description: 'Makes N (3) HTTP round trips to the CUBE this session talks to and times each, then sums up as ping does — and adds the average of this session\'s own calls to CUBE so far. Only CUBE is pinged from here: a hosted session is not a probe for the network it sits on.',
-        options: ['  -c N    Round trips to make (default 3, at most 20)'],
-        examples: ['ping', 'ping -c 10'],
-    },
-    chrisfetch: {
-        usage: 'chrisfetch',
-        summary: 'The brain beside the session\'s facts, neofetch style',
-        description: 'Who you are and where, feeds by scope, jobs run and the failure rate, the index\'s state, the surfaces attached, the uptime — beside the ChRIS brain. All from what the session already holds: no extra calls.',
-        examples: ['chrisfetch', 'chrisfetch | lolcat'],
-    },
     say: {
         usage: 'say [text]',
         summary: 'A surface with a voice speaks it',
@@ -957,38 +345,6 @@ export const helpText = {
         options: ['  -l, --list   Every term in the book'],
         examples: ['wtf is lonk', 'wtf cube pfdcm', 'wtf -l'],
     },
-    file: {
-        usage: 'file <path>...',
-        summary: 'What a file is, by its first bytes',
-        description: 'Reads a CFS file\'s head and names it by its magic: DICOM, NIfTI, gzip, PNG, JPEG, PDF, ZIP, JSON, text and more, with its size.',
-        examples: ['file 0001.dcm', 'file ~/data/*'],
-    },
-    xxd: {
-        usage: 'xxd [-s OFFSET] [-l LENGTH] <path>',
-        summary: 'A hex dump of a file',
-        description: 'The canonical hex dump — offset, sixteen bytes in pairs, the text beside — of a CFS file. 256 bytes unless -l asks for more; -s starts further in. Says how much of the file it showed.',
-        options: ['  -s OFFSET   Start at this byte (default 0)', '  -l LENGTH   Show this many bytes (default 256)'],
-        examples: ['xxd 0001.dcm', 'xxd -s 128 -l 16 0001.dcm', 'xxd -l 4096 image.nii'],
-    },
-    strings: {
-        usage: 'strings [-n MIN] [-l LIMIT] <path>',
-        summary: 'The readable runs in a file',
-        description: 'Prints the runs of printable characters, MIN (4) or longer, in a CFS file — the way to see what a binary carries. 200 lines unless -l asks for more; says how many there were.',
-        options: ['  -n MIN      Shortest run to show (default 4)', '  -l LIMIT    Most runs to show (default 200)'],
-        examples: ['strings 0001.dcm', 'strings -n 8 report.pdf'],
-    },
-    sha256sum: {
-        usage: 'sha256sum <path>...',
-        summary: 'The SHA-256 digest of a file',
-        description: 'Prints each CFS file\'s SHA-256 as hex, then its name, in the format the coreutils tool uses.',
-        examples: ['sha256sum image.nii.gz', 'sha256sum ~/uploads/*'],
-    },
-    md5sum: {
-        usage: 'md5sum <path>...',
-        summary: 'The MD5 digest of a file',
-        description: 'Prints each CFS file\'s MD5 as hex, then its name.',
-        examples: ['md5sum image.nii.gz'],
-    },
     qr: {
         usage: 'qr <text or URL>',
         summary: 'A QR code in the console, for a phone',
@@ -1107,12 +463,6 @@ export const helpText = {
         ],
         examples: ['weather', 'weather Cape Town', 'weather Boston --units imperial', 'weather Paris -d 7'],
     },
-    motd: {
-        usage: 'motd [surface]',
-        summary: 'The greeting a session gives on arrival',
-        description: 'Says who you are, how many feeds you hold, how many jobs have run and what share of them failed, and what is running now — from the session\'s own index, at no cost. While the index is still warming it says what it holds so far. A surface may name itself (motd ARGUS) and the greeting says where you arrived. Ends with a short fortune.',
-        examples: ['motd', 'motd ARGUS'],
-    },
     date: {
         usage: 'date [-u] [+FORMAT]',
         summary: 'Print the current date and time',
@@ -1129,60 +479,6 @@ export const helpText = {
         description: 'Prints a month or year calendar with today highlighted, in the spirit of UNIX cal.',
         examples: ['cal', 'cal 2026', 'cal 7 2026'],
     },
-    whereami: {
-        usage: 'whereami',
-        description: 'Print the current CUBE URL',
-        examples: ['whereami'],
-    },
-    proc: {
-        usage: 'proc <jobs|stat|feeds|refresh|retry|find|here|watch|unwatch> [args]',
-        summary: 'Job history inspector — navigate, query and monitor ChRIS pipeline execution via /proc/jobs',
-        description: '/proc/jobs is a job history inspector for every computation visible to the current ChRIS identity. Each plugin instance is a discrete job with a parent, zero or more children, a status, parameters, and a log. Jobs are grouped into feeds (pipeline runs), and the parent-child relationships form a DAG: the execution tree of a full computation. /proc/jobs exposes this as a navigable filesystem. The daemon restores an identity-scoped local topology checkpoint, validates feed visibility with CUBE, and reconciles all plugin instances in the background. Restored queries remain usable while syncing; a cold cache still guards global queries until complete. CUBE remains authoritative.',
-        subcommands: [
-            'jobs list                               List all feeds with full counter fields (default 20)',
-            'jobs list --fields id,title,erroredJobs Select columns',
-            'jobs list --sort erroredJobs --reverse  Sort by field',
-            'jobs list --table                       Tabular output',
-            'jobs list --csv                         CSV output',
-            'jobs list --all                         All feeds (no limit)',
-            'jobs list --search failed               Filter by title substring',
-            'jobs list --force                       Wait for warm-up, then list complete results',
-            'jobs inspect                            Show all available field names',
-            'stat                                   Show cache summary',
-            'stat <feed_id>                         Show raw counters + topology state for one feed',
-            'feeds <title> [--force]                Search feed titles; --force waits for warm-up',
-            'universe                               Every feed the index holds as it landed: size, status, pipeline shape; honest while warming',
-            'layout <name>                          Where a surface last laid the universe out under a layout, as the session keeps it',
-            'layout put <name> <places>             Keep a layout: node ids to [x, y, z], as JSON (surfaces put what they settle)',
-            'refresh                                Rebuild entire proc cache',
-            'refresh <feed_id>                      Rebuild cache for one feed only',
-            'retry                                  Resume a failed topology sweep at its failed page',
-            'find <id>                              Targeted instance lookup; available during warm-up',
-            'find <name> [--force]                  Name search; --force waits for warm-up',
-            'here                                   Navigate from a CFS feed/output path to its matching job',
-            'watch <feed>                           Keep a running feed live: sample it while it runs, push its DAG to every surface',
-            'watch                                  List the session\'s watches with their state',
-            'unwatch <feed>                         Release the watch on a feed',
-        ],
-        examples: [
-            'proc jobs list',
-            'proc jobs list --sort erroredJobs --reverse --table',
-            'proc jobs list --fields id,title,erroredJobs,startedJobs --all',
-            'proc jobs list --search failed',
-            'proc jobs inspect',
-            'proc stat',
-            'proc stat 899',
-            'proc feeds failed',
-            'proc universe',
-            'proc refresh',
-            'proc retry',
-            'proc find 64306',
-            'proc find pl-fshack',
-            'proc here',
-            'proc watch feed_2583',
-            'proc unwatch 2583',
-        ],
-    },
     prompt: {
         usage: 'prompt [list | <theme>]',
         description: 'List available prompt themes or switch the active theme',
@@ -1197,19 +493,6 @@ export const helpText = {
             'prompt p10k        # Switch to two-line Powerlevel10k-inspired theme',
         ],
     },
-    physicalmode: {
-        usage: 'physicalmode [on|off]',
-        description: 'Toggle or display physical filesystem mode',
-        options: [
-            'on          Enable physical mode (paths used directly)',
-            'off         Disable physical mode (use logical-to-physical mapping)',
-        ],
-        examples: [
-            'physicalmode          # Show current status',
-            'physicalmode on       # Enable physical mode',
-            'physicalmode off      # Disable physical mode',
-        ],
-    },
     timing: {
         usage: 'timing [on|off]',
         description: 'Toggle or display command timing mode',
@@ -1236,343 +519,6 @@ export const helpText = {
             'debug off             # Disable debug mode',
         ],
     },
-    parametersofplugin: {
-        usage: 'parametersofplugin <plugin_name>',
-        description: 'Display parameters for a specific plugin',
-        examples: [
-            'parametersofplugin pl-dircopy',
-            'parametersofplugin pl-simpledsapp',
-        ],
-    },
-    tree: {
-        usage: 'tree [options] [path]',
-        description: 'Display directory tree structure',
-        options: [
-            '--follow    Follow symbolic links when traversing',
-            '--path      Emit one full path per entry (grep-friendly, no tree art)',
-            '--dirs      Show directories only',
-            '--dirpath   Emit one full directory path per line',
-        ],
-        examples: [
-            'tree                  # Tree of current directory',
-            'tree /home/user/data  # Tree of specific path',
-            'tree --follow         # Follow symbolic links',
-            'tree --path           # One path per line, no decoration',
-            'tree --dirs           # Directory hierarchy only',
-            'tree --dirpath        # One directory path per line',
-        ],
-    },
-    du: {
-        usage: 'du [options] [path]',
-        description: 'Display disk usage statistics (mimics Linux du)',
-        options: [
-            '-h, --human-readable  Print sizes in human readable format',
-            '-s, --summarize       Display only total for each argument',
-            '-a, --all             Show counts for all files, not just directories',
-            '-c, --total           Produce a grand total',
-            '-d N, --max-depth=N   Print total only if N or fewer levels below',
-            '-S, --separate-dirs   Do not include size of subdirectories',
-        ],
-        examples: [
-            'du                    # Disk usage of current directory',
-            'du -h                 # Human-readable sizes (1K, 234M, 2G)',
-            'du -s /home/user/data # Summary only for specified path',
-            'du -a                 # Show all files, not just directories',
-            'du -c                 # Show grand total at end',
-            'du -d 2               # Max depth of 2 levels',
-            'du -sh                # Human-readable summary',
-        ],
-    },
-    store: {
-        usage: 'store <subcommand> [options]',
-        description: 'Browse, search, and install plugins from ChRIS peer store',
-        options: [
-            '',
-            'NOTE: The Store is an external peer ChRIS instance, not a local CUBE resource.',
-            '      Standard resource options (--all, --limit, etc.) do not apply.',
-            '',
-            'SUBCOMMANDS:',
-            '  list              Browse all plugins in the peer store',
-            '  search <query>    Search plugins by name',
-            '  install <name>    Install a plugin from the store into local CUBE',
-            '  inspect           Show current peer store URL and connection info',
-            '  set <url>         Set peer store URL (persisted to ~/.config/chell/settings.json)',
-            '  reset             Reset peer store URL to default (cube.chrisproject.org)',
-            '',
-            'INSTALL OPTIONS:',
-            '  --compute <names>     Compute resources (comma-separated)',
-            '  Use `sudo store install …` for an administrator installation.',
-            '-l                      Long listing format',
-        ],
-        examples: [
-            'store list',
-            'store search dicom',
-            'store install pl-dcm2niix',
-            'store install pl-dcm2niix-v1.2.3',
-            'store install fnndsc/pl-dcm2niix:1.2.3',
-            'store install pl-dcm2niix --compute moc',
-            'store inspect',
-            'store set https://my-cube.org/api/v1/',
-            'store reset',
-        ],
-    },
-    compute: {
-        usage: 'compute <subcommand> [options]',
-        description: 'Manage ChRIS compute resources',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-        ],
-        examples: [
-            'compute list',
-            'compute list --table',
-            'compute list --csv',
-            'compute inspect',
-        ],
-    },
-    tag: {
-        usage: 'tags <subcommand> [options]',
-        description: 'Manage ChRIS tags',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  create <name>     Create a new tag',
-            '  update <id> <name>  Rename a tag',
-            '  delete <id>       Remove a tag',
-        ],
-        examples: ['tags list', 'tags search brain', 'tags inspect', 'tag create neuro', 'tag delete 5'],
-    },
-    tags: {
-        usage: 'tags <subcommand> [options]',
-        description: 'Manage ChRIS tags',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  create <name>     Create a new tag',
-            '  update <id> <name>  Rename a tag',
-            '  delete <id>       Remove a tag',
-        ],
-        examples: ['tags list', 'tags search brain', 'tags inspect', 'tag create neuro', 'tag delete 5'],
-    },
-    record: {
-        usage: 'record <start <manifest>|stop|status>',
-        description: 'Write what this session does down as a manifest',
-        options: [
-            'SUBCOMMANDS:',
-            '  start <manifest>  Begin capturing the lines this session runs',
-            '  stop              Write the manifest and say what it holds',
-            '  status            Whether anything is recording, and how much (the default)',
-            '',
-            'A recording captures typed lines and the lines a surface mints from a press',
-            'alike. It never invents expectations: adding `expect` lines is the author\'s',
-            'act, and the one that turns a recording into a test. Identifiers a PACS line',
-            'wears on its face (PatientID, AccessionNumber, PatientName) are offered as',
-            'parameters, so the file is shareable rather than personal.',
-        ],
-        examples: [
-            'record start ~/flows/sag-cohort.mise',
-            '# … do the work, by hand or by pressing …',
-            'record stop',
-            'play ~/flows/sag-cohort.mise --param MRN=1234567',
-        ],
-    },
-    play: {
-        usage: 'play <manifest> [--param NAME=value]... [--pace <duration>] [--dry-run]',
-        description: "Run a workflow manifest: the lines an operator could have typed",
-        options: [
-            'OPTIONS:',
-            '  --param NAME=value   Supply a parameter the manifest declares (repeatable)',
-            '  --pace <duration>    Wait between lines, for watching a play at a surface',
-            '  --dry-run            Expand the lines and show them without running any',
-            '',
-            'A MANIFEST:',
-            '  # a comment',
-            '  @name         what this workflow is',
-            '  @description  one line about it',
-            '  @param        MRN            a parameter it needs',
-            '  @param        LABEL = draft  one with a default',
-            '  <any kernel line>',
-            '',
-            'PRONOUNS a line may use:',
-            '  ${gather}        every gathered member, as operands (where it was gathered FROM)',
-            '  ${gather.place}  the same members, where they LANDED in CUBE',
-            '  ${gather.first}  ${gather.last}  ${gather.3}  ${gather.size}  ${gather.name}',
-            '  ${gather.first.place}  one member, where it landed (pull takes the address, image takes the place)',
-            '  ${feed}          the feed this session most recently worked in',
-            '  ${run}           the run it most recently scheduled',
-            '  ${run.place}     where that run writes — what the next act in a chain takes',
-            '  ${query}         where its most recent PACS answer lives',
-            '  ${cwd}           where the session is standing',
-        ],
-        examples: [
-            'play ~/flows/sag-cohort.mise --param MRN=1234567',
-            'play ~/flows/sag-cohort.mise --dry-run',
-            'play ~/flows/battery.mise --pace 2s',
-        ],
-    },
-    expect: {
-        usage: 'expect <gather|feed|run|path> [<target>] <property> [<predicate> <value>] [--within <duration>]',
-        description: 'State a claim about the session, and refuse when it does not hold',
-        options: [
-            'SUBJECTS:',
-            '  gather size|pulled|name          The cohort this session is working on',
-            '  feed <id> status                 A feed, as this session indexed it',
-            '  run <instance-id> status         One plugin instance',
-            '  path <p> exists                  Whether a path is there',
-            '  path <p> count [--matching <glob>]  How many things a folder holds',
-            '  path <p> tags <TagName>          What a DICOM header says',
-            '',
-            'COMPARISONS:',
-            '  eq  ne  gt  gte  lt  lte  contains  notContains  matches',
-            '',
-            'OPTIONS:',
-            '  --within <duration>   Keep asking until the claim holds or the time is up (30s, 20m, 2h)',
-            '  --matching <glob>     Narrow a count to names matching a shell pattern',
-            '  --deep                Count beneath the folder too — a plugin files its output in a tree',
-        ],
-        examples: [
-            'expect gather size eq 14',
-            'expect run 601152 status eq finishedSuccessfully --within 20m',
-            'expect path ~/feeds/feed_4599/pl-dcm2niix_1/data count --matching "*.nii*" gt 0',
-            'expect path ~/anon tags PatientID eq anon-001',
-        ],
-    },
-    gather: {
-        usage: 'gather <subcommand> [path...]',
-        description: "Hold the set of things this session is working on",
-        options: [
-            'SUBCOMMANDS:',
-            '  list                     Show the cohort (the default)',
-            '  add <path...>            Take series, directories or files into it',
-            '  remove <path|index...>   Drop members, by path or by listed index',
-            '  clear                    Empty it, name and feed included',
-            '  name [<name>]            Read the cohort\'s name, or give it one',
-        ],
-        examples: [
-            'gather',
-            'gather add /net/pacs/queries/qid:3125/Study_1.2.3/Series_4.5.6',
-            'gather add ~/uploads/brain',
-            'gather remove 2',
-            'gather name "sag cohort"',
-        ],
-    },
-    group: {
-        usage: 'groups <subcommand> [options]',
-        description: 'Manage ChRIS user groups',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  inspect [<group>]             Show group identity, or fields when omitted',
-            '  members <group>               List users in a group',
-            '  create <name>                  [admin] Create a new group',
-            '  delete <id>                    [admin] Remove a group',
-            '  adduser <group> <user...>     [admin] Add one or more users',
-            '  removeuser <group> <user...>  [admin] Remove one or more users',
-        ],
-        examples: ['groups list', 'group members pacs_users', 'group adduser pacs_users peter.hong joe.schmo', 'group removeuser pacs_users joe.schmo'],
-    },
-    groups: {
-        usage: 'groups <subcommand> [options]',
-        description: 'Manage ChRIS user groups',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  inspect [<group>]             Show group identity, or fields when omitted',
-            '  members <group>               List users in a group',
-            '  create <name>                  [admin] Create a new group',
-            '  delete <id>                    [admin] Remove a group',
-            '  adduser <group> <user...>     [admin] Add one or more users',
-            '  removeuser <group> <user...>  [admin] Remove one or more users',
-        ],
-        examples: ['groups list', 'group members pacs_users', 'group adduser pacs_users peter.hong joe.schmo', 'group removeuser pacs_users joe.schmo'],
-    },
-    pluginmeta: {
-        usage: 'pluginmetas <subcommand> [options]',
-        description: 'Browse ChRIS plugin metadata (abstract tool identities across versions)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  plugins <id>      List all registered versions of a plugin meta',
-        ],
-        examples: ['pluginmetas list', 'pluginmetas search dircopy', 'pluginmetas inspect', 'pluginmeta plugins 12'],
-    },
-    pluginmetas: {
-        usage: 'pluginmetas <subcommand> [options]',
-        description: 'Browse ChRIS plugin metadata (abstract tool identities across versions)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  plugins <id>      List all registered versions of a plugin meta',
-        ],
-        examples: ['pluginmetas list', 'pluginmetas search dircopy', 'pluginmetas inspect', 'pluginmeta plugins 12'],
-    },
-    plugininstance: {
-        usage: 'plugininstances <subcommand> [options]',
-        description: 'Manage ChRIS plugin instances (jobs)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  cancel <id>       Cancel a running job',
-            '  delete <id>       Remove a job',
-            '  output <id>       Show output folder path',
-            '  parameters <id>   List job parameters',
-        ],
-        examples: ['jobs list', 'jobs list --all', 'jobs search status:started', 'jobs inspect', 'job cancel 42', 'job output 42'],
-    },
-    plugininstances: {
-        usage: 'plugininstances <subcommand> [options]',
-        description: 'Manage ChRIS plugin instances (jobs)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  cancel <id>       Cancel a running job',
-            '  delete <id>       Remove a job',
-            '  output <id>       Show output folder path',
-            '  parameters <id>   List job parameters',
-        ],
-        examples: ['jobs list', 'jobs list --all', 'jobs search status:started', 'jobs inspect', 'job cancel 42', 'job output 42'],
-    },
-    workflow: {
-        usage: 'workflows <subcommand> [options]',
-        description: 'Manage ChRIS workflows (pipeline executions)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  run               Run a pipeline (alias: pipeline run)',
-            '  jobs <id>         List plugin instances created by this workflow',
-            '  rename <id> <title>  Rename a workflow',
-            '  delete <id>       Remove a workflow',
-        ],
-        examples: ['workflows list', 'workflows list --all', 'workflows inspect', 'workflow jobs 7', 'workflow delete 7'],
-    },
-    workflows: {
-        usage: 'workflows <subcommand> [options]',
-        description: 'Manage ChRIS workflows (pipeline executions)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  run               Run a pipeline (alias: pipeline run)',
-            '  jobs <id>         List plugin instances created by this workflow',
-            '  rename <id> <title>  Rename a workflow',
-            '  delete <id>       Remove a workflow',
-        ],
-        examples: ['workflows list', 'workflows list --all', 'workflows inspect', 'workflow jobs 7', 'workflow delete 7'],
-    },
-    meta: { usage: 'pluginmetas <subcommand> [options]', description: 'Alias for pluginmeta/pluginmetas', options: [...RESOURCE_LIST_OPTIONS], examples: ['metas list', 'meta inspect'] },
-    metas: { usage: 'pluginmetas <subcommand> [options]', description: 'Alias for pluginmeta/pluginmetas', options: [...RESOURCE_LIST_OPTIONS], examples: ['metas list', 'meta inspect'] },
-    instance: { usage: 'plugininstances <subcommand> [options]', description: 'Alias for plugininstance/plugininstances/job/jobs', options: [...RESOURCE_LIST_OPTIONS], examples: ['instances list', 'instance cancel 42'] },
-    instances: { usage: 'plugininstances <subcommand> [options]', description: 'Alias for plugininstance/plugininstances/job/jobs', options: [...RESOURCE_LIST_OPTIONS], examples: ['instances list', 'instance cancel 42'] },
-    job: { usage: 'plugininstances <subcommand> [options]', description: 'Alias for plugininstance/plugininstances', options: [...RESOURCE_LIST_OPTIONS], examples: ['jobs list', 'job cancel 42', 'job output 42'] },
-    jobs: { usage: 'plugininstances <subcommand> [options]', description: 'Alias for plugininstance/plugininstances', options: [...RESOURCE_LIST_OPTIONS], examples: ['jobs list', 'job cancel 42', 'job output 42'] },
     help: {
         usage: 'help [command]',
         description: 'Display help information',
@@ -1594,140 +540,10 @@ export const helpText = {
             '! echo "test" > /tmp/file.txt  # Write to host file',
         ],
     },
-    dcm: {
-        usage: 'dcm <series|tags> <path> [options]',
-        summary: 'DICOM as the kernel sees it: a folder as a series, a file or folder as tags',
-        description: 'Read DICOM without leaving the session. `dcm series` answers what a folder is as a series: '
-            + 'identity, modality, instance count, stack order, geometry, transfer syntax, bytes, and any '
-            + 'annotations saved for its UID. `dcm tags` lists every element of a file, or what a folder\'s '
-            + 'files share against what changes across them. Identifying tags are marked PHI and shown; '
-            + 'a shared surface redacts them by that mark.',
-        options: [
-            'SUBCOMMANDS:',
-            '  series <folder>                 The folder as a series (one header read, order from file names)',
-            '  tags <file|folder>              Every tag of a file; constant versus varying across a folder',
-            '',
-            'OPTIONS (tags):',
-            '  --all                           Show meta and private groups too',
-            '  --filter <text>                 Only tags whose tag, name, value or decoding contains <text>',
-            '',
-            'A folder\'s tags are read from every file up to 512, then from an even sample; the listing says '
-                + 'how many were read of how many there are.',
-        ],
-        examples: [
-            'dcm series .                                  # This folder as a series',
-            'dcm series /SERVICES/PACS/PACSDCM/patient/study/00005-T1-abcdef0',
-            'dcm tags 0001-1.2.840.113619.2.55.3.1.dcm      # One file, grouped by module',
-            'dcm tags . --filter Position                   # Position tags across the folder',
-            'dcm tags . --all                               # Meta and private groups included',
-        ],
-    },
-    image: {
-        usage: 'image [--force] <path>',
-        summary: 'Show a DICOM series or a volume — a browser draws it, a terminal reflects it',
-        description: 'Open an image as the kernel sees it. `image <path>` resolves what the path is — a series '
-            + 'folder, a `.dcm` file (its folder is the series), or a NIfTI/MGZ volume — and emits an image.view '
-            + 'intent every attached surface renders in its own way: a graphical surface (ARGUS) opens a rendered '
-            + 'pane; a text surface (a shared TTY) prints a reflection — the same facts `dcm series` shows, under an '
-            + '`image` line, with a small ASCII or truecolour thumbnail of the middle slice. So the same `image` line '
-            + 'works from a browser and from a terminal sharing one CALYPSO session.',
-        options: [
-            'OPTIONS:',
-            '  --force                         Ride through the volume-size guard a graphical surface would hold at',
-        ],
-        examples: [
-            'image ~/uploads/sag-anon                      # A series folder',
-            'image /SERVICES/PACS/PACSDCM/patient/study/00005-T1-abcdef0',
-            'image scan.dcm                                # A single file; its folder is the series',
-            'image brain.nii.gz --force                    # A volume, past the size guard',
-        ],
-    },
-    cubepath: {
-        usage: 'cubepath <vfs-path> [--pacsserver <id>]',
-        description: 'Show CUBE FS path and file count for each series under a PACS VFS path. Zero files = not pulled.',
-        options: [
-            '--pacsserver <id>    Override PACS server (default: context PACSserver)',
-            '--help               Show this help',
-        ],
-        examples: [
-            '# All series under a query',
-            'cubepath /net/pacs/queries/AccessionNumber:12345678_qid:2661',
-            '',
-            '# All series under a study',
-            'cubepath /net/pacs/queries/AccessionNumber:12345678_qid:2661/Study_1.2.3_Brain_MRI',
-            '',
-            '# Single series',
-            'cubepath /net/pacs/queries/AccessionNumber:12345678_qid:2661/Study_1.2.3/Series_1.2.3.4_AX_T2',
-        ],
-    },
-    query: {
-        usage: 'query <Key:Value[,Key:Value...]> [--patients <list|@cfs-file>] [--title <title>] [--pacsserver <id>] [--fresh]',
-        description: 'Create a PACS query, wait for results, and print the VFS path',
-        options: [
-            '--title <title>      Title for the query record (default: Query <timestamp>)',
-            '--pacsserver <id>    Override PACS server (default: context PACSserver)',
-            '--table              Render results as a table instead of the default list',
-            '--fresh              Ask the PACS even if this question was answered before',
-            '--help               Show this help',
-        ],
-        examples: [
-            'query PatientID:1234',
-            'query PatientID:1234 --fresh           # ignore the stored answer',
-            'query AccessionNumber:12345678 --title "Hip DDH workup"',
-            'query PatientID:1234,StudyDate:20240101',
-            '',
-            '# A PACS matches one patient at a time, so several MRNs is several queries',
-            'query PatientID:1234,4532,6654         # three questions, one table',
-            'query --patients @~/cohorts/ddh.txt    # a cohort from a file in ChRIS',
-            'query StudyDate:20240101 --patients 1234,4532   # narrowed, per patient',
-            'query PatientID:1234 --pacsserver PACSDCM,ORTHANC   # ask both, one listing',
-            '',
-            '# A cohort audit, as a table a spreadsheet reads',
-            'query --patients @~/cohorts/ddh.txt --csv > audit.csv    # a local terminal',
-            'query --patients @~/cohorts/ddh.txt --csv-to ~/audits/ddh.csv   # any surface',
-            '',
-            '# Use output path directly with pull',
-            'pull $(query PatientID:1234 | grep "VFS path" | awk \'{print $3}\')',
-        ],
-    },
-    pull: {
-        usage: 'pull [--detach] [--retry N] [--new-feed <title> [--plugin <selector>|--pipeline <selector>] [-- <args...>]] <vfs-path|query-expr> [...]',
-        description: 'Pull PACS series into ChRIS storage; accepts VFS paths or query expressions (blocking)',
-        options: [
-            '--detach      Fire retrieves and return the handles at once; prints <seriesUID> <retrieveId> per line',
-            '              (--nowait is the older spelling of the same flag)',
-            '--retry N     Re-fire retrieves for [NO LONK] series up to N additional times',
-            '--new-feed <title>  Create one named feed from the complete retrieved selection',
-            '--plugin <selector> Attach one plugin to the new Feed root',
-            '--pipeline <selector> Attach one pipeline to the new Feed root',
-            '-- <args...>        Forward remaining tokens to the selected analysis',
-            '                    (cannot be combined with --detach)',
-            '--help        Show this help',
-        ],
-        examples: [
-            '# Pull all series in a query (blocking)',
-            'pull /net/pacs/queries/42_AccessionNumber:12345678',
-            '',
-            '# Pull a single study',
-            'pull /net/pacs/queries/42_AccessionNumber:12345678/Study_1.2.3_US-Hips_DDH',
-            '',
-            '# Pull a specific series',
-            'pull /net/pacs/queries/42_AccessionNumber:12345678/Study_1.2.3_US-Hips_DDH/Series_1.2.3.4_XR',
-            '',
-            '# Pull multiple paths in one blocking call',
-            'pull /net/pacs/queries/42_AccessionNumber:12345678 /net/pacs/queries/43_PatientID:P001',
-            '',
-            '# Pull directly from a query expression (creates query, waits, then pulls)',
-            'pull PatientID:1234',
-            'pull AccessionNumber:12345678',
-            'pull AccessionNumber:12345678 --new-feed "Brain MRI"',
-            '',
-            '# Detached: take the handles and carry on',
-            'pull --detach /net/pacs/queries/42_AccessionNumber:12345678',
-            '# Output: <seriesUID> <retrieveId>  (one per series, in tree-walk order)',
-        ],
-    },
 };
+// The help is registered with the engine's commands; every reader below goes
+// through the registry, never this record.
+commands_register({ help: helpText });
 /**
  * Displays help text for a command.
  *
@@ -1850,7 +666,7 @@ function commandHelp_render(command, help) {
  * @returns The formatted help text string, or undefined if no help exists.
  */
 export function commandHelp_get(command) {
-    const help = helpText[command];
+    const help = commandHelpEntry_get(command);
     return help ? commandHelp_render(command, help) : undefined;
 }
 /**
@@ -1931,8 +747,35 @@ export function help_render(command) {
     if (helpStr !== undefined) {
         return `${helpStr}\n`;
     }
+    return helpMissing_render(command);
+}
+/**
+ * The page for a name with no help in this session.
+ *
+ * @param command - The name asked about.
+ * @returns The page.
+ */
+export function helpMissing_render(command) {
     return `${chalk.yellow(`No help available for '${command}'`)}\n${chalk.gray('Type "help" to see all available commands.')}\n`;
 }
+/** Words the shell or its surface answers itself, with no handler in the registry. */
+const SHELL_WORDS = ['exit', '!', 'help', 'prompt'];
+/**
+ * Whether this session can run a verb (or a verb's subcommand, `pacs query`):
+ * its handler is registered (the core's, or its backend's), or the shell
+ * answers it. Help is shown only for what can be run.
+ *
+ * @param name - The command, perhaps with a subcommand.
+ * @returns True when the session has it.
+ */
+export function verb_available(name) {
+    const verb = name.split(' ')[0] ?? '';
+    if (SHELL_WORDS.includes(verb))
+        return true;
+    if (verb === 'sudo')
+        return backendInstalled_get()?.elevate !== undefined;
+    return builtinCommand_has(verb);
+}
 /**
  * Checks if arguments contain --help flag.
  * -h is treated as help unless the command uses it for "human-readable" (ls, du).
@@ -1974,11 +817,14 @@ export async function builtin_help(args) {
         return builtin_notes([]);
     }
     // If a specific command is requested, return its help
+    // A verb this session has; else whatever its backend answers for (ChRIS:
+    // a plugin or pipeline executable); else no help, never a page for a verb
+    // the session cannot run.
     if (commandName) {
-        if (/-v[^/]+$/.test(commandName)) {
-            return { status: 'ok', rendered: pluginExecutableHelp_render(commandName) };
-        }
-        return { status: 'ok', rendered: help_render(commandName) };
+        if (verb_available(commandName))
+            return { status: 'ok', rendered: help_render(commandName) };
+        const backendHelp = (await backendInstalled_get()?.fallback?.help?.(commandName)) ?? null;
+        return { status: 'ok', rendered: backendHelp ?? helpMissing_render(commandName) };
     }
     // Otherwise, list all available commands
     let rendered = '';
@@ -2004,9 +850,12 @@ export async function builtin_help(args) {
     };
     // Display commands by category
     for (const [category, commands] of Object.entries(categories)) {
+        const runnable = commands.filter((cmd) => verb_available(cmd) && commandHelpEntry_get(cmd) !== undefined);
+        if (runnable.length === 0 && category !== 'Games and utilities')
+            continue;
         rendered += `${chalk.bold.yellow(category)}\n`;
-        commands.forEach((cmd) => {
-            const help = helpText[cmd];
+        runnable.forEach((cmd) => {
+            const help = commandHelpEntry_get(cmd);
             if (help) {
                 rendered += `  ${chalk.cyan(cmd.padEnd(20))} ${chalk.gray(help.summary ?? help.description)}\n`;
             }
@@ -2014,7 +863,7 @@ export async function builtin_help(args) {
         // The four above are the shelf's best known; the rest of /usr/games is
         // its own page, and the count is read from the shelf so it never goes stale.
         if (category === 'Games and utilities') {
-            const more = gamesShelf_names(commandSummary_get).length - commands.length;
+            const more = gamesShelf_names(commandSummary_get).length - runnable.length;
             rendered += `  ${chalk.cyan('help games'.padEnd(20))} ${chalk.gray(`The /usr/games shelf by category: ${more} more small tools and games`)}\n`;
         }
         rendered += '\n';
@@ -2036,7 +885,9 @@ export async function builtin_help(args) {
  * @returns Array of builtin command names.
  */
 export function builtinCommands_list() {
-    return Object.keys(helpText);
+    // `/usr/bin` and completion offer what this session can run, never a
+    // backend's verbs it does not have.
+    return helpTopic_names().filter((name) => verb_available(name));
 }
 /**
  * A command's one-line summary (its `summary`, else its description), for
@@ -2046,7 +897,7 @@ export function builtinCommands_list() {
  * @returns The line, or undefined for a command with no help entry.
  */
 export function commandSummary_get(command) {
-    const help = helpText[command];
+    const help = commandHelpEntry_get(command);
     return help === undefined ? undefined : (help.summary ?? help.description);
 }
 /**
@@ -2056,6 +907,6 @@ export function commandSummary_get(command) {
  * @returns The command description, or undefined if not found.
  */
 export function builtinCommand_descriptionGet(command) {
-    return helpText[command]?.description;
+    return commandHelpEntry_get(command)?.description;
 }
 //# sourceMappingURL=help.js.map