@fnndsc/brasa 0.9.1 → 0.10.0

package/dist/builtins/fs/rm.js.map

@@ -1 +1 @@
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package/dist/builtins/fs/tree.js

@@ -24,9 +24,13 @@ import { bytes_format } from '@fnndsc/chili/commands/fs/upload.js';
  * ```
  */
 export async function builtin_tree(args) {
-    const parsed = commandArgs_process(args);
+    const parsed = commandArgs_process(args, {
+        booleanLongOptions: ['follow', 'path', 'dirs', 'dirpath'],
+    });
     const pathArgs = parsed._;
-    const pathMode = !!parsed['path'];
+    const dirpathMode = !!parsed['dirpath'];
+    const pathMode = !!parsed['path'] || dirpathMode;
+    const dirsOnly = !!parsed['dirs'] || dirpathMode;
     // Determine target path
     let targetPath;
     if (pathArgs.length > 0) {
@@ -37,7 +41,7 @@ export async function builtin_tree(args) {
         silent: true,
         tree: false, // We'll format it ourselves
         follow: !!parsed['follow'],
-        dirsOnly: false,
+        dirsOnly,
     };
     // If path specified, temporarily set context
     const originalFolder = await session.getCWD();

package/dist/builtins/fs/tree.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tree.js","sourceRoot":"","sources":["../../../src/builtins/fs/tree.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAc,mBAAmB,EAAE,YAAY,EAAE,sBAAsB,EAAE,MAAM,aAAa,CAAC;AACpG,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AAC/C,OAAO,EAAE,UAAU,EAAmB,WAAW,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AACzF,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAiC,MAAM,mCAAmC,CAAC;AAC7G,OAAO,EAAE,YAAY,EAAE,MAAM,qCAAqC,CAAC;AAEnE;;;;;;;;;;;;;GAaG;AACH,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,IAAc;IAC/C,MAAM,MAAM,GAAe,mBAAmB,CAAC,IAAI,EAAE;QACnD,kBAAkB,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,CAAC;KAC1D,CAAC,CAAC;IACH,MAAM,QAAQ,GAAa,MAAM,CAAC,CAAa,CAAC;IAChD,MAAM,WAAW,GAAY,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IACjD,MAAM,QAAQ,GAAY,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,WAAW,CAAC;IAC1D,MAAM,QAAQ,GAAY,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,WAAW,CAAC;IAE1D,wBAAwB;IACxB,IAAI,UAA8B,CAAC;IACnC,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,UAAU,GAAG,MAAM,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;IAED,qBAAqB;IACrB,MAAM,WAAW,GAAY;QAC3B,MAAM,EAAE,IAAI;QACZ,IAAI,EAAE,KAAK,EAAG,4BAA4B;QAC1C,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC;QAC1B,QAAQ;KACT,CAAC;IAEF,6CAA6C;IAC7C,MAAM,cAAc,GAAW,MAAM,OAAO,CAAC,MAAM,EAAE,CAAC;IACtD,IAAI,UAAU,EAAE,CAAC;QACf,MAAM,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC;IACnC,CAAC;IAED,IAAI,CAAC;QACH,OAAO,CAAC,KAAK,CAAC,YAAY,UAAU,IAAI,mBAAmB,KAAK,CAAC,CAAC;QAClE,MAAM,UAAU,GAAsB,MAAM,OAAO,CAAC,WAAW,CAAC,CAAC;QAEjE,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,CAAC,IAAI,EAAE,CAAC;YACf,MAAM,SAAS,GAAG,UAAU,CAAC,SAAS,EAAE,CAAC;YACzC,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;YACrB,MAAM,OAAO,GAAW,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,gCAAgC,CAAC;YACjH,OAAO,cAAc,CAAC,EAAE,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;QAClE,CAAC;QAED,OAAO,CAAC,IAAI,EAAE,CAAC;QAEf,IAAI,QAAQ,GAAW,EAAE,CAAC;QAC1B,IAAI,QAAQ,EAAE,CAAC;YACb,4DAA4D;YAC5D,KAAK,MAAM,IAAI,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;gBACvC,QAAQ,IAAI,GAAG,IAAI,CAAC,SAAS,IAAI,CAAC;YACpC,CAAC;QACH,CAAC;aAAM,CAAC;YACN,sBAAsB;YACtB,QAAQ,IAAI,GAAG,gBAAgB,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC;QAC3D,CAAC;QAED,kBAAkB;QAClB,QAAQ,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,eAAe,YAAY,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC,IAAI,CAAC;QACpF,QAAQ,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,QAAQ,CAAC,IAAI,CAAC;QACrE,OAAO,WAAW,CAAC,QAAQ,CAAC,CAAC;IAE/B,CAAC;YAAS,CAAC;QACT,wBAAwB;QACxB,IAAI,UAAU,EAAE,CAAC;YACf,MAAM,OAAO,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC;QACvC,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/builtins/fs/upload.js

@@ -7,6 +7,21 @@ import { path_resolve } from '../utils.js';
 import { files_uploadWithProgress as chefs_upload_cmd, bytes_format } from '@fnndsc/chili/commands/fs/upload.js';
 import { listCache_get, envelope_ok, envelope_error } from '@fnndsc/cumin';
 import { sink_get } from '../../core/sink.js';
+import { shellArguments_pathnameExpansion } from '../../lib/parser.js';
+import { surface_get } from '../../core/surface.js';
+/**
+ * Asks the issuing surface to confirm replacement of an existing CFS target.
+ *
+ * @param message - Confirmation question prepared by the transfer command.
+ * @returns Nothing when the surface accepts the operation.
+ * @throws {Error} When the surface declines the operation.
+ */
+async function uploadConfirmation_request(message) {
+    const answer = await surface_get().prompt({ message });
+    if (answer.trim().toLowerCase() !== 'y' && answer.trim().toLowerCase() !== 'yes') {
+        throw new Error('Operation cancelled by user.');
+    }
+}
 /**
  * Uploads a local file or directory to ChRIS.
  *
@@ -19,9 +34,19 @@ export async function builtin_upload(args) {
     }
     const localPath = args[0];
     const remotePath = args[1];
+    const localGlob = shellArguments_pathnameExpansion(args, 0);
     const targetRemote = await path_resolve(remotePath);
     try {
         const summary = await chefs_upload_cmd(localPath, targetRemote, {
+            expandLocalGlob: localGlob,
+            confirm: uploadConfirmation_request,
+            onNotice: (message, channel) => {
+                const sink = sink_get();
+                if (channel === 'status')
+                    sink.status_write(`${message}\n`);
+                else
+                    sink.err_write(`${message}\n`);
+            },
             onProgress: event => sink_get().progress_write(event),
         });
         let rendered = '\n';
@@ -32,10 +57,12 @@ export async function builtin_upload(args) {
             rendered += `${chalk.yellow(`⚠ Uploaded ${summary.transferredCount} file(s), ${summary.failedCount} failed`)}\n`;
         }
         rendered += `${chalk.gray(`  Total: ${bytes_format(summary.transferSize)} in ${summary.duration.toFixed(1)}s (${bytes_format(summary.speed)}/s)`)}\n`;
-        // Invalidate cache for actual target directory where files were uploaded
+        // Invalidate cache for actual target directory where files were uploaded,
+        // including nested listings: a directory re-upload replaces a whole tree,
+        // and still-fresh entries below the target would serve the old contents.
         if (summary.transferredCount > 0) {
             const listCache = listCache_get();
-            listCache.cache_invalidate(summary.actualTargetPath);
+            listCache.cache_invalidateTree(summary.actualTargetPath);
             // Also invalidate parent to refresh its listing
             listCache.cache_invalidate(targetRemote);
         }

package/dist/builtins/fs/upload.js.map

@@ -1 +1 @@
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+{"version":3,"file":"upload.js","sourceRoot":"","sources":["../../../src/builtins/fs/upload.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,EAAE,wBAAwB,IAAI,gBAAgB,EAAiB,YAAY,EAAE,MAAM,qCAAqC,CAAC;AAChI,OAAO,EAAE,aAAa,EAAwB,WAAW,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AAEjG,OAAO,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAC9C,OAAO,EAAE,gCAAgC,EAAE,MAAM,qBAAqB,CAAC;AACvE,OAAO,EAAE,WAAW,EAAE,MAAM,uBAAuB,CAAC;AAEpD;;;;;;GAMG;AACH,KAAK,UAAU,0BAA0B,CAAC,OAAe;IACvD,MAAM,MAAM,GAAW,MAAM,WAAW,EAAE,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC;IAC/D,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,KAAK,GAAG,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,KAAK,KAAK,EAAE,CAAC;QACjF,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAC;IAClD,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAc;IACjD,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACpB,OAAO,WAAW,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,0CAA0C,CAAC,IAAI,CAAC,CAAC;IACnF,CAAC;IACD,MAAM,SAAS,GAAW,IAAI,CAAC,CAAC,CAAC,CAAC;IAClC,MAAM,UAAU,GAAW,IAAI,CAAC,CAAC,CAAC,CAAC;IACnC,MAAM,SAAS,GAAY,gCAAgC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAErE,MAAM,YAAY,GAAW,MAAM,YAAY,CAAC,UAAU,CAAC,CAAC;IAE5D,IAAI,CAAC;QACH,MAAM,OAAO,GAAkB,MAAM,gBAAgB,CAAC,SAAS,EAAE,YAAY,EAAE;YAC7E,eAAe,EAAE,SAAS;YAC1B,OAAO,EAAE,0BAA0B;YACnC,QAAQ,EAAE,CAAC,OAAe,EAAE,OAAyB,EAAQ,EAAE;gBAC7D,MAAM,IAAI,GAAG,QAAQ,EAAE,CAAC;gBACxB,IAAI,OAAO,KAAK,QAAQ;oBAAE,IAAI,CAAC,YAAY,CAAC,GAAG,OAAO,IAAI,CAAC,CAAC;;oBACvD,IAAI,CAAC,SAAS,CAAC,GAAG,OAAO,IAAI,CAAC,CAAC;YACtC,CAAC;YACD,UAAU,EAAE,KAAK,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,cAAc,CAAC,KAAK,CAAC;SACtD,CAAC,CAAC;QAEH,IAAI,QAAQ,GAAW,IAAI,CAAC;QAC5B,IAAI,OAAO,CAAC,WAAW,KAAK,CAAC,EAAE,CAAC;YAC9B,QAAQ,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,2BAA2B,OAAO,CAAC,gBAAgB,UAAU,CAAC,IAAI,CAAC;QAChG,CAAC;aAAM,CAAC;YACN,QAAQ,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,cAAc,OAAO,CAAC,gBAAgB,aAAa,OAAO,CAAC,WAAW,SAAS,CAAC,IAAI,CAAC;QACnH,CAAC;QACD,QAAQ,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,YAAY,YAAY,CAAC,OAAO,CAAC,YAAY,CAAC,OAAO,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,YAAY,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC;QAEtJ,0EAA0E;QAC1E,0EAA0E;QAC1E,yEAAyE;QACzE,IAAI,OAAO,CAAC,gBAAgB,GAAG,CAAC,EAAE,CAAC;YACjC,MAAM,SAAS,GAAG,aAAa,EAAE,CAAC;YAClC,SAAS,CAAC,oBAAoB,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC;YACzD,gDAAgD;YAChD,SAAS,CAAC,gBAAgB,CAAC,YAAY,CAAC,CAAC;QAC3C,CAAC;QACD,OAAO,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC/B,CAAC;IAAC,OAAO,CAAU,EAAE,CAAC;QACpB,MAAM,GAAG,GAAW,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QAC/D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO,cAAc,CAAC,EAAE,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC,GAAG,CAAC,iBAAiB,GAAG,EAAE,CAAC,IAAI,CAAC,CAAC;IACjF,CAAC;AACH,CAAC"}

package/dist/builtins/help.d.ts

@@ -48,6 +48,13 @@ export declare function commandHelp_get(command: string): string | undefined;
  * @returns Pipeline-specific help text, terminated with a newline.
  */
 export declare function pipelineExecutableHelp_render(name: string): string;
+/**
+ * Renders contextual help for one versioned plugin executable.
+ *
+ * @param name - Plugin executable name as exposed in `/bin`.
+ * @returns Plugin-specific help text, terminated with a newline.
+ */
+export declare function pluginExecutableHelp_render(name: string): string;
 /**
  * Renders a command's help text as a string.
  *

package/dist/builtins/help.js

@@ -6,6 +6,7 @@
  * @module
  */
 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.
@@ -30,6 +31,24 @@ export const RESOURCE_LIST_OPTIONS = [
  * 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',
+        options: [
+            'Prompts for an administrator username and hidden password on the active surface.',
+            'The elevated CUBE token is used only for the nested command; it is not saved or made the session identity.',
+        ],
+        examples: [
+            'sudo group adduser pacs_users peter.hong',
+            'sudo plugin add pl-dircopy',
+        ],
+    },
     ls: {
         usage: 'ls [options] [path]',
         description: 'List directory contents',
@@ -86,12 +105,20 @@ export const helpText = {
         ],
     },
     cat: {
-        usage: 'cat <file> [file...]',
-        description: 'Display file contents',
+        usage: CAT_USAGE,
+        description: 'Display file contents, with terminal syntax highlighting for recognized text formats',
+        options: [
+            '--binary              Force byte-for-byte binary output',
+            '--highlight           Force highlighting; infer the language from the filename or content',
+            '--highlight=LANGUAGE  Force a cli-highlight language such as python, typescript, or sql',
+            '--no-highlight        Disable automatic syntax highlighting',
+        ],
         examples: [
-            'cat file.txt          # Display single file',
-            'cat file1 file2       # Display multiple files',
-            'cat *.log             # Display all .log files (wildcard)',
+            'cat file.txt                    # Display single file',
+            'cat analysis.py                 # Auto-highlight Python in a terminal',
+            'cat source --highlight=python   # Force Python highlighting without filename inference',
+            'cat config.json --no-highlight  # Display raw text',
+            'cat file1 file2                 # Display multiple files',
         ],
     },
     edit: {
@@ -136,6 +163,12 @@ export const helpText = {
         description: 'Copy files or directories (supports wildcards and multiple sources)',
         options: [
             '-r, --recursive    Recursive copy (for directories)',
+            '',
+            'PACS SOURCES: a /net/pacs/queries/... source names query results, not',
+            'stored files. cp MATERIALIZES the series: if its DICOMs are not yet in',
+            'CUBE it fires a PACS retrieve and waits for them to land (the same',
+            'engine as pull), then copies the landed files to the destination.',
+            'A series already fully in CUBE is copied without a retrieve.',
         ],
         examples: [
             'cp file.txt copy.txt              # Copy single file',
@@ -143,6 +176,8 @@ export const helpText = {
             'cp file1 file2 file3 dest/        # Copy multiple files',
             'cp uploads/*.txt backup/          # Copy with wildcard',
             'cp "file with spaces.txt" dest/   # Use quotes for spaces',
+            'cp -r /net/pacs/queries/AccessionNumber:123_qid:7/Study_1.2.3_Head/Series_1.2.3.4_AX_T2 results/',
+            '                                  # Retrieve-if-needed, then copy the series',
         ],
     },
     mv: {
@@ -180,8 +215,8 @@ export const helpText = {
         ],
     },
     upload: {
-        usage: 'upload <local_path> <chris_path>',
-        description: 'Upload files from local filesystem to ChRIS with progress tracking',
+        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',
@@ -191,19 +226,21 @@ export const helpText = {
         ],
         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> <local_path> [-f|--force]',
-        description: 'Download a ChRIS file or directory to the local filesystem with progress tracking',
+        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',
         ],
     },
@@ -292,8 +329,8 @@ export const helpText = {
             'PLUGINS ADD OPTIONS:',
             '  --compute <resources>         Comma-separated compute resources (default: host)',
             '  --store <url>                 Peer store URL (default: cube.chrisproject.org)',
-            '  --adminUser <username>        Admin username (to skip interactive prompt)',
-            '  --adminPassword <password>    Admin password (to skip interactive prompt)',
+            '  --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:',
@@ -322,8 +359,8 @@ export const helpText = {
             'plugins add pl-dircopy',
             'plugins add pl-dircopy --compute host,gpu',
             '',
-            '# Add plugin with admin credentials (skip prompt)',
-            'plugins add pl-dircopy --adminUser chris --adminPassword chris1234',
+            '# 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',
@@ -432,6 +469,7 @@ export const helpText = {
             '',
             'RESOURCE-SPECIFIC SUBCOMMANDS:',
             '  info <name|id>        Show pipeline nodes, plugins, and topology',
+            '  manifest <name|id|slug>  Emit complete registered invocation YAML',
             '  run <name|id>         Execute pipeline on current context node',
             '  source <name|id>      Display the pipeline YAML source file',
             '  diagram <name|id>     Draw the pipeline as a shallow tree',
@@ -442,23 +480,31 @@ export const helpText = {
             'RUN OPTIONS:',
             '  --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>     Same as pipeline source',
+            '  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',
@@ -468,9 +514,10 @@ export const helpText = {
             '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                 # Same as --source',
+            'cat /bin/PHI_detection                 # Cached executable summary',
         ],
     },
     pacs: {
@@ -484,6 +531,8 @@ export const helpText = {
             '  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',
@@ -494,6 +543,7 @@ export const helpText = {
             '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': {
@@ -515,17 +565,23 @@ export const helpText = {
         ],
     },
     'pacs pull': {
-        usage: 'pacs pull [--nowait] [--retry N] <vfs-path|query-expr> [...]',
+        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: [
             '--nowait      Fire retrieves and exit immediately; prints <seriesUID> <retrieveId> per line',
             '--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 --nowait)',
             '--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',
@@ -602,6 +658,11 @@ export const helpText = {
         description: 'Print the currently authenticated ChRIS username',
         examples: ['whoami'],
     },
+    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',
@@ -630,9 +691,9 @@ export const helpText = {
         examples: ['whereami'],
     },
     proc: {
-        usage: 'proc <jobs|stat|feeds|refresh|find> [args]',
+        usage: 'proc <jobs|stat|feeds|refresh|retry|find|here> [args]',
         summary: 'Job history inspector — navigate, query and monitor ChRIS pipeline execution via /proc/jobs',
-        description: '/proc/jobs is a job history inspector. Every computation ever run in ChRIS is a plugin instance — 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. cd into a feed to see what ran. ls -l shows job status at a glance. tree shows the full execution DAG. cat status, cat log, cat params give you CUBE data as plain text — no API queries to write, no UI to open. The in-memory cache makes this instant: built at login from the feed index, warmed in the background across all plugin instances. Once warm, all navigation, search, and path reconstruction are zero-cost in-memory operations.',
+        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',
@@ -641,13 +702,17 @@ export const helpText = {
             '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>                          Search feed titles; returns /proc/jobs/feed_N paths',
+            'feeds <title> [--force]                Search feed titles; --force waits for warm-up',
             'refresh                                Rebuild entire proc cache',
             'refresh <feed_id>                      Rebuild cache for one feed only',
-            'find <id|name>                         Find instance by ID or plugin name substring',
+            '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',
         ],
         examples: [
             'proc jobs list',
@@ -659,8 +724,10 @@ export const helpText = {
             'proc stat 899',
             'proc feeds failed',
             'proc refresh',
+            'proc retry',
             'proc find 64306',
             'proc find pl-fshack',
+            'proc here',
         ],
     },
     prompt: {
@@ -730,12 +797,16 @@ export const helpText = {
         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: {
@@ -777,8 +848,7 @@ export const helpText = {
             '',
             'INSTALL OPTIONS:',
             '  --compute <names>     Compute resources (comma-separated)',
-            '  --adminUser <user>    Admin username for install',
-            '  --adminPassword <pw>  Admin password for install',
+            '  Use `sudo store install …` for an administrator installation.',
             '-l                      Long listing format',
         ],
         examples: [
@@ -839,13 +909,14 @@ export const helpText = {
             ...RESOURCE_LIST_OPTIONS,
             '',
             'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  members <id>          List users in a group',
-            '  create <name>         [admin] Create a new group',
-            '  delete <id>           [admin] Remove a group',
-            '  adduser <id> <user>   [admin] Add user to group',
-            '  removeuser <id> <user> [admin] Remove user from group',
-        ],
-        examples: ['groups list', 'groups search all_users', 'groups inspect', 'group members 3'],
+            '  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]',
@@ -854,13 +925,14 @@ export const helpText = {
             ...RESOURCE_LIST_OPTIONS,
             '',
             'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  members <id>          List users in a group',
-            '  create <name>         [admin] Create a new group',
-            '  delete <id>           [admin] Remove a group',
-            '  adduser <id> <user>   [admin] Add user to group',
-            '  removeuser <id> <user> [admin] Remove user from group',
-        ],
-        examples: ['groups list', 'groups search all_users', 'groups inspect', 'group members 3'],
+            '  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]',
@@ -1003,11 +1075,16 @@ export const helpText = {
         ],
     },
     pull: {
-        usage: 'pull [--nowait] <vfs-path|query-expr> [...]',
+        usage: 'pull [--nowait] [--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: [
             '--nowait      Fire retrieves and exit immediately; prints <seriesUID> <retrieveId> per line',
             '--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 --nowait)',
             '--help        Show this help',
         ],
         examples: [
@@ -1026,6 +1103,7 @@ export const helpText = {
             '# Pull directly from a query expression (creates query, waits, then pulls)',
             'pull PatientID:1234',
             'pull AccessionNumber:12345678',
+            'pull AccessionNumber:12345678 --new-feed "Brain MRI"',
             '',
             '# Fire-and-forget (scripted)',
             'pull --nowait /net/pacs/queries/42_AccessionNumber:12345678',
@@ -1178,21 +1256,49 @@ export function pipelineExecutableHelp_render(name) {
             'INSPECTION:',
             '  --nodes, --parameters   Show pipeline nodes and parameters',
             '  --source, --readme      Show the pipeline YAML source',
+            '  --manifest              Emit complete registered invocation YAML',
             '',
             'EXECUTION:',
             '  --compute <resource>    Override the compute resource',
             '  --previous <inst_id>    Attach to an explicit plugin instance',
+            '  --paramFile <cfs-file>  Apply one sparse YAML invocation overlay',
+            '  --<node>.<parameter> <value>  Override a hosted parameter',
+            '  --<node>.<control> <value>    Override a node execution control',
         ],
         examples: [
             `${name} --diagram`,
             `${name} --diagram --withargs`,
             `${name} --signalflow | signalflow -`,
             `${name} --source`,
+            `${name} --manifest`,
             `${name} --previous 123`,
         ],
     };
     return `${commandHelp_render(name, help)}\n`;
 }
+/**
+ * Renders contextual help for one versioned plugin executable.
+ *
+ * @param name - Plugin executable name as exposed in `/bin`.
+ * @returns Plugin-specific help text, terminated with a newline.
+ */
+export function pluginExecutableHelp_render(name) {
+    const help = {
+        usage: `${name} <operation>`,
+        description: 'Inspect this registered CUBE plugin version.',
+        options: [
+            '  --parameters   Show parameter definitions for this plugin version',
+            '  --readme       Show the rendered plugin README',
+            '  --readme --raw Output raw README markdown for piping',
+        ],
+        examples: [
+            `${name} --parameters`,
+            `${name} --readme`,
+            `${name} --readme --raw | glow -`,
+        ],
+    };
+    return `${commandHelp_render(name, help)}\n`;
+}
 /**
  * Renders a command's help text as a string.
  *
@@ -1241,6 +1347,9 @@ export async function builtin_help(args) {
     const commandName = args.length > 0 ? args.join(' ') : undefined;
     // If a specific command is requested, return its help
     if (commandName) {
+        if (/-v[^/]+$/.test(commandName)) {
+            return { status: 'ok', rendered: pluginExecutableHelp_render(commandName) };
+        }
         return { status: 'ok', rendered: help_render(commandName) };
     }
     // Otherwise, list all available commands
@@ -1253,11 +1362,12 @@ export async function builtin_help(args) {
     const categories = {
         Navigation: ['cd', 'pwd', 'ls', 'tree', 'du'],
         'File Operations': ['cat', 'edit', 'cp', 'mv', 'rm', 'touch', 'mkdir', 'upload', 'download'],
-        Connection: ['connect', 'logout', 'context', 'whoami', 'whereami'],
+        Connection: ['connect', 'logout', 'context', 'id', 'whoami', 'whereami'],
         Monitoring: ['proc'],
         'Single Resource': ['plugin', 'pipeline', 'feed', 'tag', 'group', 'pluginmeta', 'plugininstance', 'workflow'],
         'Resource Collections': ['plugins', 'feeds', 'files', 'links', 'dirs', 'store', 'compute', 'tags', 'groups', 'pluginmetas', 'plugininstances', 'workflows', 'parametersofplugin'],
         PACS: ['pacs', 'pacsservers', 'pacsqueries', 'pacsretrieve'],
+        Administration: ['sudo', 'user'],
         'Shell Settings': ['physicalmode', 'prompt', 'timing', 'debug'],
         General: ['help', 'date', 'cal', 'fortune', 'exit', '!'],
     };