@rho-workspace/rho 0.5.5 → 0.5.7

package/dist/plugin-inventory.json

@@ -5,6 +5,7 @@
       "id": "documents",
       "package": "@rho-workspace/plugin-documents",
       "version": "0.4.7",
+      "packageVersion": "0.4.11",
       "requires": [],
       "presentation": {
         "categoryOrder": 10,
@@ -42,8 +43,12 @@
         "runsCode": false
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "document.open",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 10,
               "displayName": "Open",
@@ -53,6 +58,10 @@
             }
           },
           {
+            "method": "document.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 20,
               "displayName": "Read",
@@ -62,6 +71,10 @@
             }
           },
           {
+            "method": "document.edit",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 30,
               "displayName": "Edit",
@@ -71,6 +84,10 @@
             }
           },
           {
+            "method": "document.undo",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 40,
               "displayName": "Undo",
@@ -80,6 +97,10 @@
             }
           },
           {
+            "method": "document.undoOwn",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 41,
               "displayName": "Undo my edits",
@@ -89,6 +110,10 @@
             }
           },
           {
+            "method": "document.revert",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 42,
               "displayName": "Revert one change",
@@ -98,6 +123,10 @@
             }
           },
           {
+            "method": "document.history",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 21,
               "displayName": "Read change history",
@@ -107,6 +136,10 @@
             }
           },
           {
+            "method": "document.change.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 22,
               "displayName": "Read a change",
@@ -116,6 +149,10 @@
             }
           },
           {
+            "method": "document.save",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 50,
               "displayName": "Save",
@@ -125,6 +162,10 @@
             }
           },
           {
+            "method": "document.abandonSave",
+            "version": "2.0",
+            "effect": "document",
+            "requires": [],
             "presentation": {
               "order": 60,
               "displayName": "Give up an interrupted save",
@@ -134,11 +175,15 @@
             }
           }
         ],
+        "actions": [],
         "views": [
           {
             "id": "rho.editor",
             "version": "0.2.0",
             "ui": "./ui",
+            "bindings": {
+              "document": "document"
+            },
             "presentation": {
               "description": "Shows the shared code or note buffer in a layout.",
               "displayName": "Editor",
@@ -152,18 +197,94 @@
             "id": "documents.workspace",
             "version": "1.4",
             "digest": "e93fa01d13fc8dbd920a11d8944c3fc1e2e4b7760ed9f713c45bdc6d3f8f27dd",
+            "intent": "Edit a document buffer conditionally, with explicit undo and save conditions.",
+            "requires": [
+              "document.open",
+              "document.read",
+              "document.edit",
+              "document.save",
+              "document.undoOwn",
+              "document.revert"
+            ],
+            "example": {
+              "method": "document.edit",
+              "input": {
+                "documentId": "5df1e6280c70fa8475dfd6bb1a6165b302443640224c893510eed728058adac0",
+                "expectedVersion": 1,
+                "expectedRevision": 0,
+                "changeId": "edit-intro-1",
+                "undoGroup": "agent-edit",
+                "edits": [
+                  {
+                    "from": 0,
+                    "to": 0,
+                    "insert": "# Draft\n"
+                  }
+                ]
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "invalid",
+                "message": "must have property expectedRevision when property changeId is present",
+                "next": "Send changeId and expectedRevision together; read the buffer for its current revision."
+              },
+              {
+                "kind": "stale",
+                "message": "Document version or revision changed.",
+                "next": "Re-read the document and retry with its current version and revision; keep the original changeId only for the same request."
+              },
+              {
+                "kind": "scope",
+                "message": "Internal state is not an editable document.",
+                "next": "Edit a project file, not anything under .rho or .git."
+              },
+              {
+                "kind": "condition",
+                "message": "Resume the original pending save before changing this buffer.",
+                "next": "Read the buffer, then resume that exact save or abandon it with document.abandonSave."
+              },
+              {
+                "kind": "unauthorized",
+                "message": "Only the Agent or operator saves to disk.",
+                "next": "A tab edits the buffer; ask the Agent to save the document."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:documents",
+              "description": "Author-scoped undo, one-change revert, shared buffers and conditional saves over HTTP."
+            },
             "presentation": {
               "displayName": "Document workspace",
               "description": "Teaches Claude Code to use the shared buffer, preserve undo and check for changes before saving."
             }
           }
-        ]
+        ],
+        "claudeCode": {
+          "skills": [
+            {
+              "skill": "documents.workspace",
+              "name": "documents",
+              "description": "Change a project file that is open in Rho through its shared buffer (document.read, document.edit, document.save), so a person's unsaved text, undo and saves stay intact."
+            }
+          ],
+          "hooks": [
+            {
+              "id": "documents.unsaved-text",
+              "event": "PreToolUse",
+              "matcher": "Edit|Write|MultiEdit",
+              "entry": "./claude-hook",
+              "timeoutSeconds": 10
+            }
+          ]
+        }
       }
     },
     {
       "id": "files",
       "package": "@rho-workspace/plugin-files",
       "version": "0.5.0",
+      "packageVersion": "0.5.1",
       "requires": [],
       "presentation": {
         "categoryOrder": 40,
@@ -201,8 +322,12 @@
         "runsCode": false
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "resource.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 10,
               "displayName": "List",
@@ -212,6 +337,10 @@
             }
           },
           {
+            "method": "resource.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 20,
               "displayName": "Read",
@@ -221,6 +350,10 @@
             }
           },
           {
+            "method": "resource.register",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 30,
               "displayName": "Register",
@@ -230,6 +363,10 @@
             }
           },
           {
+            "method": "artifact.check",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 40,
               "displayName": "Check outputs",
@@ -239,6 +376,10 @@
             }
           },
           {
+            "method": "resource.capture",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 15,
               "displayName": "Capture a version",
@@ -248,12 +389,78 @@
             }
           }
         ],
+        "actions": [],
         "views": [],
         "skills": [
           {
             "id": "files.workspace",
             "version": "1.1",
             "digest": "e285f2c5fd9dab58732726ee4fe71006e49d2c2ebea1a9e95b511077ae136fba",
+            "intent": "Register existing bytes with explicit identity, read them bounded, and verify produced artifacts.",
+            "requires": [
+              "resource.register",
+              "resource.read",
+              "resource.list",
+              "artifact.check"
+            ],
+            "example": {
+              "method": "resource.register",
+              "input": {
+                "expectedDigest": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+                "declaration": {
+                  "path": "data/points.csv",
+                  "kind": "table",
+                  "format": {
+                    "encoding": "csv",
+                    "columns": [
+                      {
+                        "name": "id",
+                        "type": "string",
+                        "nullValues": []
+                      },
+                      {
+                        "name": "value",
+                        "type": "number",
+                        "nullValues": [
+                          "",
+                          "NA"
+                        ]
+                      }
+                    ],
+                    "key": {
+                      "column": "id",
+                      "namespace": "samples"
+                    }
+                  }
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "stale",
+                "message": "Registered bytes no longer match the declaration digest.",
+                "next": "Re-read the file and register the current digest as a new version; keep the old one for what already cited it."
+              },
+              {
+                "kind": "scope",
+                "message": "Register a project file outside internal state.",
+                "next": "Register project files only; an artifact under .rho is checked with artifact.check."
+              },
+              {
+                "kind": "invalid",
+                "message": "Declared columns do not match the file.",
+                "next": "Declare every column with its type and the null values that mean missing."
+              },
+              {
+                "kind": "condition",
+                "message": "No complete artifact inventory has been declared.",
+                "next": "Have the producer write the completion inventory, then call artifact.check."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:files",
+              "description": "A completion sidecar verifies immutable producer bytes, escaping output declarations are refused, and declared output directories exist before the producer runs."
+            },
             "presentation": {
               "displayName": "File workspace",
               "description": "Teaches Claude Code to register versioned files, read bounded bytes and check declared outputs."
@@ -266,6 +473,7 @@
       "id": "r",
       "package": "@rho-workspace/plugin-r",
       "version": "0.4.1",
+      "packageVersion": "0.4.2",
       "requires": [
         "files"
       ],
@@ -313,8 +521,14 @@
         "runsCode": true
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "object.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [
+              "files"
+            ],
             "presentation": {
               "order": 10,
               "displayName": "Read an exported object",
@@ -324,6 +538,29 @@
             }
           },
           {
+            "method": "action.submit",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [
+              "files",
+              "requirements"
+            ],
+            "presentation": {
+              "order": 20,
+              "displayName": "Run a script",
+              "description": "Runs a saved script or your unsaved edits, with the inputs it names.",
+              "readOnly": false,
+              "runsCode": true
+            }
+          }
+        ],
+        "actions": [
+          {
+            "id": "r.execute",
+            "version": "0.2.0",
+            "requires": [
+              "requirements"
+            ],
             "presentation": {
               "order": 20,
               "displayName": "Run a script",
@@ -338,6 +575,9 @@
             "id": "rho.object",
             "version": "0.2.0",
             "ui": "unavailable",
+            "bindings": {
+              "data": "object"
+            },
             "presentation": {
               "description": "Shows an exported object in a layout, next to the code and data.",
               "displayName": "Object",
@@ -351,6 +591,70 @@
             "id": "r.workspace",
             "version": "1.1",
             "digest": "199a9517030682b6568b6139e1d535f59806d0efd96daa5f40c918a8310d6d8e",
+            "intent": "Run an R script in this project and keep its produced artifacts.",
+            "requires": [
+              "action.submit",
+              "action.lookup",
+              "artifact.check"
+            ],
+            "example": {
+              "method": "action.submit",
+              "input": {
+                "operationId": "analysis-1",
+                "action": "r.execute",
+                "actionVersion": "0.2.0",
+                "input": {
+                  "script": {
+                    "kind": "disk",
+                    "path": "R/plot.R",
+                    "digest": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
+                  },
+                  "args": [],
+                  "requirements": [],
+                  "artifacts": [
+                    {
+                      "path": "cars.png",
+                      "kind": "file",
+                      "format": {
+                        "mimeType": "image/png"
+                      }
+                    }
+                  ],
+                  "completion": "inventory.json"
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "scope",
+                "message": "Use a project-relative path without parent traversal.",
+                "next": "Address the script and every artifact inside the project; the run output directory is the only writable output location."
+              },
+              {
+                "kind": "stale",
+                "message": "Saved script bytes changed before submission.",
+                "next": "Re-read the script, take its current digest, and submit once with that digest."
+              },
+              {
+                "kind": "not_found",
+                "message": "Requested owner record or file is missing.",
+                "next": "Look the operation up from the session that submitted it; facts are keyed by principal."
+              },
+              {
+                "kind": "condition",
+                "message": "No complete artifact inventory has been declared.",
+                "next": "Declare completion and write that inventory from the producer before calling artifact.check."
+              },
+              {
+                "kind": "unavailable",
+                "message": "Requested executable is unavailable.",
+                "next": "Select the Core binary and Rscript explicitly, then retry the same operation identity."
+              }
+            ],
+            "verify": {
+              "command": "npm run acceptance:execution",
+              "description": "Submits r.execute for a script that writes an artifact into the directory it is handed, then asserts one Host start, the artifact, its completion inventory and artifact.check."
+            },
             "presentation": {
               "displayName": "R workspace",
               "description": "Teaches Claude Code to read exported objects and to start runs it can find again later."
@@ -363,6 +667,7 @@
       "id": "requirements",
       "package": "@rho-workspace/plugin-requirements",
       "version": "0.4.0",
+      "packageVersion": "0.4.2",
       "requires": [],
       "presentation": {
         "categoryOrder": 10,
@@ -402,8 +707,12 @@
         "runsCode": true
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "requirements.check",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 10,
               "displayName": "Check",
@@ -413,6 +722,10 @@
             }
           },
           {
+            "method": "requirements.prepare",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
             "presentation": {
               "order": 20,
               "displayName": "Install into the project",
@@ -422,12 +735,50 @@
             }
           }
         ],
+        "actions": [],
         "views": [],
         "skills": [
           {
             "id": "requirements.workspace",
             "version": "1.1",
             "digest": "3dcdc17236c087068750a8da7061c57d9737a7f8ff1db775a63deb36a2155045",
+            "intent": "Know whether an R script can run here before submitting it.",
+            "requires": [
+              "requirements.check",
+              "requirements.prepare"
+            ],
+            "example": {
+              "method": "requirements.check",
+              "input": {
+                "requirements": [
+                  {
+                    "package": "digest",
+                    "source": "cran"
+                  }
+                ]
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "unavailable",
+                "message": "R is unavailable.",
+                "next": "Select an existing Rscript with --rscript or RHO_RSCRIPT; the check reports unknown rather than failing the service."
+              },
+              {
+                "kind": "invalid",
+                "message": "Package declaration is malformed.",
+                "next": "Declare each package by name with source cran or bioconductor."
+              },
+              {
+                "kind": "limit",
+                "message": "Too many declared packages.",
+                "next": "Declare the packages the script truly needs; the limit is explicit in the reply."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:requirements",
+              "description": "Empty and base-R requirements need no add-on package, and script and argument references are checked before dispatch."
+            },
             "presentation": {
               "displayName": "Requirements workspace",
               "description": "Teaches Claude Code to check declared dependencies and prepare missing packages explicitly."
@@ -439,7 +790,8 @@
     {
       "id": "tables",
       "package": "@rho-workspace/plugin-tables",
-      "version": "0.5.0",
+      "version": "0.5.2",
+      "packageVersion": "0.5.2",
       "requires": [
         "files"
       ],
@@ -485,8 +837,14 @@
         "runsCode": false
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "data.page",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [
+              "files"
+            ],
             "presentation": {
               "order": 10,
               "displayName": "Page, sort and filter",
@@ -496,6 +854,12 @@
             }
           },
           {
+            "method": "data.compare",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "files"
+            ],
             "presentation": {
               "order": 20,
               "displayName": "Compare two tables",
@@ -505,11 +869,15 @@
             }
           }
         ],
+        "actions": [],
         "views": [
           {
             "id": "rho.table",
             "version": "0.2.0",
             "ui": "./ui",
+            "bindings": {
+              "data": "table"
+            },
             "presentation": {
               "description": "Shows table rows with their declared types and stable keys.",
               "displayName": "Table",
@@ -523,6 +891,53 @@
             "id": "tables.workspace",
             "version": "1.1",
             "digest": "c5da9fda0f6fb8db603de57d9f0132ac5620193ba4d72af1c635d6087dd7b3b9",
+            "intent": "Page and compare a typed table without inventing identity from row order.",
+            "requires": [
+              "resource.register",
+              "data.page",
+              "data.compare"
+            ],
+            "example": {
+              "method": "data.page",
+              "input": {
+                "resource": {
+                  "id": "4702434457c0465d6dfbb54793b62d327c9aa4f419be2f5fc6cf92c6918eeaf1",
+                  "version": "3f9d2b0e1a4c5f6d7e8f90a1b2c3d4e5f60718293a4b5c6d7e8f90a1b2c3d4e5"
+                },
+                "offset": 0,
+                "limit": 50,
+                "sort": {
+                  "column": "score",
+                  "direction": "desc"
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "stale",
+                "message": "Resource version changed.",
+                "next": "Register or re-read the current version; save the new {id, version} before paging again."
+              },
+              {
+                "kind": "limit",
+                "message": "Page size exceeds the configured limit.",
+                "next": "Ask for fewer rows; the earlier rows stay readable."
+              },
+              {
+                "kind": "invalid",
+                "message": "Filter or sort names an unknown column.",
+                "next": "Use a declared column name from the registration, not a positional index."
+              },
+              {
+                "kind": "condition",
+                "message": "Compare needs two keyed tables in declared namespaces.",
+                "next": "Declare a key column and namespace at registration before comparing."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:tables",
+              "description": "Declared types keep leading zeros and literal NA, joins retain nulls, namespaces and both input versions, and unkeyed tables never fabricate keys."
+            },
             "presentation": {
               "displayName": "Table workspace",
               "description": "Teaches Claude Code to use declared types, stable keys and exact table versions."
@@ -535,6 +950,7 @@
       "id": "media",
       "package": "@rho-workspace/plugin-media",
       "version": "0.4.0",
+      "packageVersion": "0.4.0",
       "requires": [
         "files"
       ],
@@ -580,8 +996,14 @@
         "runsCode": false
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "media.describe",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [
+              "files"
+            ],
             "presentation": {
               "order": 10,
               "displayName": "Describe an image or PDF and check regions",
@@ -591,11 +1013,15 @@
             }
           }
         ],
+        "actions": [],
         "views": [
           {
             "id": "rho.media",
             "version": "0.2.0",
             "ui": "./ui",
+            "bindings": {
+              "data": "media"
+            },
             "presentation": {
               "description": "Shows an image or PDF with its original source reference.",
               "displayName": "Media",
@@ -609,6 +1035,42 @@
             "id": "media.workspace",
             "version": "1.1",
             "digest": "0a0f6bfd15daef696a399e855a23fb53d25a6ad8b964e02ac5029e23ac8ebaeb",
+            "intent": "Describe media and select a region in original coordinates.",
+            "requires": [
+              "media.describe",
+              "resource.register",
+              "object.read"
+            ],
+            "example": {
+              "method": "media.describe",
+              "input": {
+                "resource": {
+                  "id": "9f1c2d3e4b5a69788796a5b4c3d2e1f00112233445566778899aabbccddeeff0",
+                  "version": "3f9d2b0e1a4c5f6d7e8f90a1b2c3d4e5f60718293a4b5c6d7e8f90a1b2c3d4e5"
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "invalid",
+                "message": "Region lies outside the declared media bounds.",
+                "next": "Use coordinates inside width and height from the registration; a region is never clamped."
+              },
+              {
+                "kind": "stale",
+                "message": "Resource version changed.",
+                "next": "Re-register the current bytes and describe the new version."
+              },
+              {
+                "kind": "unavailable",
+                "message": "This build selects no renderer.",
+                "next": "Describe and select stay available; only rendering is missing."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:media",
+              "description": "Registers media, maps a selection to original coordinates, and refuses a region outside the declared bounds."
+            },
             "presentation": {
               "displayName": "Media workspace",
               "description": "Teaches Claude Code to inspect original media metadata and validate coordinate regions."
@@ -621,6 +1083,7 @@
       "id": "charts",
       "package": "@rho-workspace/plugin-charts",
       "version": "0.4.0",
+      "packageVersion": "0.4.0",
       "requires": [
         "tables"
       ],
@@ -679,8 +1142,14 @@
         "runsCode": false
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "data.plot",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [
+              "tables"
+            ],
             "presentation": {
               "order": 10,
               "displayName": "Plot two numeric columns",
@@ -690,11 +1159,15 @@
             }
           }
         ],
+        "actions": [],
         "views": [
           {
             "id": "rho.scatter",
             "version": "0.2.0",
             "ui": "./ui",
+            "bindings": {
+              "data": "table"
+            },
             "presentation": {
               "description": "Shows a scatter plot whose points trace to their source rows.",
               "displayName": "Scatter",
@@ -708,6 +1181,50 @@
             "id": "charts.workspace",
             "version": "1.1",
             "digest": "44077df075458acf1b04464fc8fdf5fce9e5528a5f1cee4b73d68fa71b34a867",
+            "intent": "Plot two numeric columns of one table version, bounded and reproducible.",
+            "requires": [
+              "data.plot",
+              "data.page",
+              "resource.register"
+            ],
+            "example": {
+              "method": "data.plot",
+              "input": {
+                "resource": {
+                  "id": "4702434457c0465d6dfbb54793b62d327c9aa4f419be2f5fc6cf92c6918eeaf1",
+                  "version": "3f9d2b0e1a4c5f6d7e8f90a1b2c3d4e5f60718293a4b5c6d7e8f90a1b2c3d4e5"
+                },
+                "x": "value",
+                "y": "value",
+                "maxPoints": 1000
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "condition",
+                "message": "Entity interaction requires an explicit unique key and namespace.",
+                "next": "Register the table with a key column and namespace before plotting it."
+              },
+              {
+                "kind": "invalid",
+                "message": "Declare numeric scatter coordinate fields.",
+                "next": "Name two columns declared as number; a string column cannot be a coordinate."
+              },
+              {
+                "kind": "stale",
+                "message": "Resource version changed.",
+                "next": "Re-register the current bytes and plot the new version."
+              },
+              {
+                "kind": "limit",
+                "message": "Plot request exceeds the point budget.",
+                "next": "Lower maxPoints or accept the deterministic downsample the reply reports."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:charts",
+              "description": "A plot names the exact table version it read, downsamples to the point budget, and a changed file makes the version stale."
+            },
             "presentation": {
               "displayName": "Chart workspace",
               "description": "Teaches Claude Code to bind chart columns and keep point selections tied to stable rows."
@@ -716,10 +1233,203 @@
         ]
       }
     },
+    {
+      "id": "annotations",
+      "package": "@rho-workspace/plugin-annotations",
+      "version": "0.5.2",
+      "packageVersion": "0.5.2",
+      "requires": [
+        "documents"
+      ],
+      "presentation": {
+        "categoryOrder": 30,
+        "order": 20,
+        "description": "Comments attach to an exact code range or table entity and preserve the source version they refer to. Claude Code can read them and explicitly link a reply; making a comment available does not claim the Agent has read it.",
+        "icon": {
+          "background": "#FBF2D8",
+          "color": "#8A6A10",
+          "paths": [
+            "M5 5h14a1 1 0 0 1 1 1v9a1 1 0 0 1-1 1h-8l-4 3v-3H5a1 1 0 0 1-1-1V6a1 1 0 0 1 1-1z"
+          ]
+        },
+        "dependencies": [
+          {
+            "pluginId": "documents",
+            "purpose": "to freeze comment and reply messages"
+          }
+        ],
+        "developer": "Rho",
+        "license": "AGPL-3.0-only",
+        "links": [
+          {
+            "label": "Source",
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/annotations"
+          },
+          {
+            "label": "Privacy",
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/blob/main/PRIVACY.md"
+          }
+        ],
+        "displayName": "Annotations",
+        "tagline": "Comments the Agent can read and answer",
+        "category": "Working with your Agent",
+        "examplePrompts": [
+          "“Read my comments on clean.R and reply to each one.”",
+          "“List the comments in this project that have no reply yet.”",
+          "“Leave a note on line 42 of fit.R explaining the change.”"
+        ],
+        "viewNote": "Inside other views",
+        "readOnly": false,
+        "runsCode": false
+      },
+      "listing": {
+        "operations": [
+          {
+            "method": "annotation.create",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "documents"
+            ],
+            "presentation": {
+              "order": 10,
+              "displayName": "Create",
+              "description": "Submits a comment with its exact source anchor and message.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "annotation.reply",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "documents"
+            ],
+            "presentation": {
+              "order": 40,
+              "displayName": "Reply",
+              "description": "Links an explicit reply to a submitted comment.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "annotation.decide",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "documents"
+            ],
+            "presentation": {
+              "displayName": "Record decision",
+              "description": "Records the person’s decision about exact result versions.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "annotation.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [
+              "documents"
+            ],
+            "presentation": {
+              "order": 30,
+              "displayName": "Read",
+              "description": "Reads a comment and its retained source context.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "annotation.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [
+              "documents"
+            ],
+            "presentation": {
+              "order": 20,
+              "displayName": "List",
+              "description": "Lists comments and their reply state.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          }
+        ],
+        "actions": [],
+        "views": [
+          {
+            "id": "rho.feedback",
+            "version": "0.2.0",
+            "ui": "./ui",
+            "bindings": {
+              "draft": "document"
+            },
+            "presentation": {
+              "displayName": "Feedback",
+              "description": "Asks about selected objects and follows original delivery and linked replies.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          }
+        ],
+        "skills": [
+          {
+            "id": "annotations.workspace",
+            "version": "1.1",
+            "digest": "e4bcb4b32ff641e040f2ebda2259f75bdb2765afae49273325f63852c5a1bef7",
+            "presentation": {
+              "displayName": "Annotation workspace",
+              "description": "Teaches Claude Code to preserve versioned anchors and link replies to submitted comments."
+            },
+            "intent": "Submit and follow anchored feedback without rebasing the original message.",
+            "requires": [
+              "annotation.create",
+              "annotation.read",
+              "annotation.list",
+              "annotation.reply",
+              "context.create",
+              "context.read"
+            ],
+            "example": {
+              "method": "annotation.list",
+              "input": {
+                "projectId": "the-open-project"
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "stale",
+                "message": "Anchor or thread advanced past the submitted version.",
+                "next": "Read the thread, then reply with an explicit replyTo instead of moving the original anchor."
+              },
+              {
+                "kind": "scope",
+                "message": "Selection or anchor is outside this binding.",
+                "next": "Anchor inside the document or table the binding owns."
+              },
+              {
+                "kind": "invalid",
+                "message": "Anchor range or entity key is malformed.",
+                "next": "Use UTF-16 offsets for documents and a declared entity key for tables."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:annotations",
+              "description": "Submits anchored messages over versioned drafts, advances threads conditionally and keeps original snapshots."
+            }
+          }
+        ]
+      }
+    },
     {
       "id": "agent",
       "package": "@rho-workspace/plugin-agent",
-      "version": "0.4.19",
+      "version": "0.4.33",
+      "packageVersion": "0.4.33",
       "requires": [],
       "presentation": {
         "categoryOrder": 30,
@@ -767,8 +1477,12 @@
         "runsCode": false
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "agent.sessions.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 58,
               "displayName": "External conversations",
@@ -778,6 +1492,10 @@
             }
           },
           {
+            "method": "agent.sessions.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 59,
               "displayName": "External conversation",
@@ -787,6 +1505,10 @@
             }
           },
           {
+            "method": "agent.activity.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 62,
               "displayName": "Agent activity",
@@ -796,6 +1518,10 @@
             }
           },
           {
+            "method": "agent.activity.outputs",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 63,
               "displayName": "Observed outputs",
@@ -805,6 +1531,12 @@
             }
           },
           {
+            "method": "agent.activity.capture",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "files"
+            ],
             "presentation": {
               "order": 64,
               "displayName": "Open observed output",
@@ -814,6 +1546,10 @@
             }
           },
           {
+            "method": "context.create",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 10,
               "displayName": "Share and read context",
@@ -823,6 +1559,10 @@
             }
           },
           {
+            "method": "context.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 20,
               "displayName": "Share and read context",
@@ -832,6 +1572,10 @@
             }
           },
           {
+            "method": "binding.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 30,
               "displayName": "Open and close views",
@@ -841,6 +1585,10 @@
             }
           },
           {
+            "method": "binding.activity",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 60,
               "displayName": "Activity",
@@ -850,6 +1598,10 @@
             }
           },
           {
+            "method": "binding.open",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 40,
               "displayName": "Open and close views",
@@ -859,6 +1611,10 @@
             }
           },
           {
+            "method": "binding.close",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 50,
               "displayName": "Open and close views",
@@ -868,6 +1624,13 @@
             }
           },
           {
+            "method": "feedback.submit",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "documents",
+              "annotations"
+            ],
             "presentation": {
               "order": 70,
               "displayName": "Feedback",
@@ -877,6 +1640,12 @@
             }
           },
           {
+            "method": "feedback.read",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [
+              "annotations"
+            ],
             "presentation": {
               "order": 71,
               "displayName": "Feedback",
@@ -886,6 +1655,10 @@
             }
           },
           {
+            "method": "feedback.status",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 72,
               "displayName": "Feedback",
@@ -895,6 +1668,10 @@
             }
           },
           {
+            "method": "binding.activity.append",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
             "presentation": {
               "order": 61,
               "displayName": "Activity",
@@ -904,11 +1681,13 @@
             }
           }
         ],
+        "actions": [],
         "views": [
           {
             "id": "rho.agent-note",
             "version": "0.2.0",
             "ui": "./ui",
+            "bindings": {},
             "presentation": {
               "displayName": "Agent note",
               "description": "A plain presentation explanation with authenticated author and binding basis.",
@@ -922,6 +1701,46 @@
             "id": "agent.workspace",
             "version": "1.2",
             "digest": "0228d41b186fd5fd622156b6f7f30ff524c66573006bb822b72cb1060746730a",
+            "intent": "Give a native session exact prepared context and keep its binding identity.",
+            "requires": [
+              "context.create",
+              "context.read",
+              "binding.open",
+              "binding.list",
+              "binding.activity"
+            ],
+            "example": {
+              "method": "context.create",
+              "input": {
+                "document": {
+                  "documentId": "5df1e6280c70fa8475dfd6bb1a6165b302443640224c893510eed728058adac0",
+                  "version": 1,
+                  "from": 0,
+                  "to": 12
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "stale",
+                "message": "Context source version changed.",
+                "next": "Build a new context from the current version; do not edit through an old snapshot."
+              },
+              {
+                "kind": "scope",
+                "message": "Binding belongs to a different task or principal.",
+                "next": "Use the binding issued for this task and role; a forged attachment is refused."
+              },
+              {
+                "kind": "unavailable",
+                "message": "No native adapter is registered.",
+                "next": "Ask the operator to register the adapter for this project before opening a binding."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:native",
+              "description": "Registers a native adapter, opens a business binding, refuses a forged one, and records artifact-ready observations without a model call."
+            },
             "presentation": {
               "displayName": "Agent workspace",
               "description": "Teaches Claude Code to fetch explicit context and preserve the original identity of changes."
@@ -931,6 +1750,50 @@
             "id": "agent.feedback",
             "version": "1.1",
             "digest": "9b38022bd4d6566f3112ace0f756b3e56855740f9de6afbe14d5851550d5ee2f",
+            "intent": "Read one original feedback delivery and answer it explicitly.",
+            "requires": [
+              "feedback.read",
+              "feedback.status",
+              "document.read",
+              "document.edit",
+              "annotation.reply"
+            ],
+            "example": {
+              "method": "feedback.read",
+              "input": {
+                "taskId": "grades",
+                "deliveryId": "delivery-1",
+                "contextId": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+                "fetchId": "fetch-1",
+                "query": {
+                  "after": 0,
+                  "cursor": null,
+                  "limit": 50,
+                  "maxBytes": 65536
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "limit",
+                "message": "Feedback object exceeds maxBytes.",
+                "next": "Increase maxBytes and read the whole object; never use a partial message."
+              },
+              {
+                "kind": "stale",
+                "message": "Related document changed since the feedback.",
+                "next": "Read the current document version and edit conditionally, keeping human changes."
+              },
+              {
+                "kind": "unauthorized",
+                "message": "Only the original business binding may read this delivery.",
+                "next": "Read it from the binding that received the delivery."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:feedback",
+              "description": "Drives the real feedback worker and hook entries without a model: original delivery, whole-object fetch and explicit reply."
+            },
             "presentation": {
               "displayName": "Business feedback",
               "description": "Reads original feedback, preserves current human edits and links an explicit reply."
@@ -940,151 +1803,248 @@
             "id": "agent.presentation",
             "version": "1.1",
             "digest": "89cf29d839abc32d8730465e8c635b0c24d14dee4b624a881db68f48d4e79920",
+            "intent": "Enhance the visible layout for the assigned presenter, display only.",
+            "requires": [
+              "workspace.observe",
+              "workspace.enhance"
+            ],
+            "example": {
+              "method": "workspace.observe",
+              "input": {
+                "taskId": "grades",
+                "compositionId": "workspace",
+                "query": {
+                  "after": 0,
+                  "cursor": null,
+                  "limit": 20,
+                  "maxBytes": 65536
+                }
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "stale",
+                "message": "Witness, generation or layout changed.",
+                "next": "Observe again and form an explicit new intent; never rebase silently."
+              },
+              {
+                "kind": "scope",
+                "message": "Presentation role cannot reach business feedback or documents.",
+                "next": "Stay within workspace.observe and workspace.enhance."
+              },
+              {
+                "kind": "limit",
+                "message": "Note exceeds 600 characters.",
+                "next": "Shorten the note; emphasis and title carry the rest."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:presenter",
+              "description": "Presentation enhances display within its witness and role, and refuses business feedback or document access."
+            },
             "presentation": {
               "displayName": "Presentation",
               "description": "Enhances the assigned visible layout without business feedback or document access."
             }
           }
-        ]
+        ],
+        "cli": [
+          "rho-agent-observe",
+          "rho-agent-mcp",
+          "rho-agent-acp"
+        ],
+        "mcp": {
+          "entry": "./mcp",
+          "transport": "stdio",
+          "tools": [
+            {
+              "name": "rho_index",
+              "description": "Discover optional Rho workspace capabilities alongside your native tools. Core managed execution is chosen only when needed. Select owner or search to page authorized operations. No full schemas are loaded."
+            },
+            {
+              "name": "rho_resolve",
+              "description": "Fetch complete guidance and contracts only for selected operations. Follow whole-object pages; knownRefs reuse bodies you still hold."
+            },
+            {
+              "name": "rho_call",
+              "description": "Call one resolved authorized operation. Large replies return an immutable result reference for rho_read; never repeat a write to retrieve its output."
+            },
+            {
+              "name": "rho_read",
+              "description": "Inspect a retained result by JSON pointer, page containers or text, or explicitly release it. Text offsets count UTF-16 units. Reading never invokes the original operation."
+            }
+          ]
+        }
       }
     },
     {
-      "id": "annotations",
-      "package": "@rho-workspace/plugin-annotations",
-      "version": "0.5.2",
-      "requires": [
-        "documents"
-      ],
+      "id": "console",
+      "package": "@rho-workspace/plugin-console",
+      "version": "0.3.0",
+      "packageVersion": "0.3.1",
+      "requires": [],
       "presentation": {
         "categoryOrder": 30,
-        "order": 20,
-        "description": "Comments attach to an exact code range or table entity and preserve the source version they refer to. Claude Code can read them and explicitly link a reply; making a comment available does not claim the Agent has read it.",
+        "order": 30,
+        "description": "The Console lists the commands run in a project — the Agent's, from its own reports, and yours — with how each ended, how long it took and what it printed. You can run a command in the project folder yourself, run one again or stop it. It runs only for the person at this machine.",
         "icon": {
-          "background": "#FBF2D8",
-          "color": "#8A6A10",
+          "background": "#E8ECEF",
+          "color": "#3E4C57",
           "paths": [
-            "M5 5h14a1 1 0 0 1 1 1v9a1 1 0 0 1-1 1h-8l-4 3v-3H5a1 1 0 0 1-1-1V6a1 1 0 0 1 1-1z"
+            "M4.5 5.5h15a1 1 0 0 1 1 1v11a1 1 0 0 1-1 1h-15a1 1 0 0 1-1-1v-11a1 1 0 0 1 1-1z",
+            "m7.5 9.5 2.5 2.5-2.5 2.5",
+            "M12 14.5h4.5"
           ]
         },
-        "dependencies": [
-          {
-            "pluginId": "documents",
-            "purpose": "to freeze comment and reply messages"
-          }
-        ],
+        "dependencies": [],
         "developer": "Rho",
         "license": "AGPL-3.0-only",
         "links": [
           {
             "label": "Source",
-            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/annotations"
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/console"
           },
           {
             "label": "Privacy",
             "url": "https://github.com/YuLab-SMU/Rho-plugins/blob/main/PRIVACY.md"
           }
         ],
-        "displayName": "Annotations",
-        "tagline": "Comments the Agent can read and answer",
+        "displayName": "Console",
+        "tagline": "Every command run in the project, and yours",
         "category": "Working with your Agent",
         "examplePrompts": [
-          "“Read my comments on clean.R and reply to each one.”",
-          "“List the comments in this project that have no reply yet.”",
-          "“Leave a note on line 42 of fit.R explaining the change.”"
+          "“Run the analysis script again and show me what it printed.”",
+          "“Which command wrote results/summary.csv?”",
+          "“Why did the last command fail?”"
         ],
-        "viewNote": "Inside other views",
+        "viewNote": "Its own page in each project",
         "readOnly": false,
-        "runsCode": false
+        "runsCode": true
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "console.run",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
             "presentation": {
               "order": 10,
-              "displayName": "Create",
-              "description": "Submits a comment with its exact source anchor and message.",
+              "displayName": "Run a command",
+              "description": "Runs a command you typed in the project folder and keeps what it prints.",
               "readOnly": false,
-              "runsCode": false
+              "runsCode": true
             }
           },
           {
+            "method": "console.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
-              "order": 40,
-              "displayName": "Reply",
-              "description": "Links an explicit reply to a submitted comment.",
-              "readOnly": false,
+              "order": 20,
+              "displayName": "List commands",
+              "description": "Lists the commands run here, newest first, with how each ended.",
+              "readOnly": true,
               "runsCode": false
             }
           },
           {
+            "method": "console.events",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
-              "displayName": "Record decision",
-              "description": "Records the person’s decision about exact result versions.",
-              "readOnly": false,
-              "runsCode": false
-            }
-          },
-          {
-            "presentation": {
-              "order": 30,
-              "displayName": "Read",
-              "description": "Reads a comment and its retained source context.",
+              "order": 25,
+              "displayName": "Read who ran what",
+              "description": "Lists the commands run here, newest first: who ran each, when, in which folder and how it ended.",
               "readOnly": true,
               "runsCode": false
             }
           },
           {
+            "method": "console.output",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
-              "order": 20,
-              "displayName": "List",
-              "description": "Lists comments and their reply state.",
+              "order": 30,
+              "displayName": "Read output",
+              "description": "Reads what a command printed, page by page.",
               "readOnly": true,
               "runsCode": false
             }
-          }
-        ],
-        "views": [
+          },
           {
-            "id": "rho.feedback",
-            "version": "0.2.0",
-            "ui": "./ui",
+            "method": "console.stop",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
             "presentation": {
-              "displayName": "Feedback",
-              "description": "Asks about selected objects and follows original delivery and linked replies.",
+              "order": 40,
+              "displayName": "Stop a command",
+              "description": "Asks a running command and the processes it started to stop.",
               "readOnly": false,
               "runsCode": false
             }
           }
         ],
+        "actions": [],
+        "views": [],
         "skills": [
           {
-            "id": "annotations.workspace",
-            "version": "1.1",
-            "digest": "e4bcb4b32ff641e040f2ebda2259f75bdb2765afae49273325f63852c5a1bef7",
+            "id": "console.workspace",
+            "version": "1.0",
+            "digest": "519f869fbf9a1384f0d592ecf5db93c16516f96b90b95304646dd6d9b8798b59",
             "presentation": {
-              "displayName": "Annotation workspace",
-              "description": "Teaches Claude Code to preserve versioned anchors and link replies to submitted comments."
+              "displayName": "Console",
+              "description": "Explains what the console records and that it runs commands only for the person."
+            },
+            "intent": "Read the commands the person ran and how they ended.",
+            "requires": [
+              "console.list",
+              "console.output"
+            ],
+            "example": {
+              "method": "console.list",
+              "input": {
+                "limit": 20
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "limit",
+                "message": "Too many commands are running.",
+                "next": "Stop one or wait for it to end, then run again with a new changeId."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:console",
+              "description": "Runs, reads and stops commands and keeps their identity across a lost response and a restart."
             }
           }
         ]
       }
     },
     {
-      "id": "console",
-      "package": "@rho-workspace/plugin-console",
-      "version": "0.3.0",
+      "id": "kernel",
+      "package": "@rho-workspace/plugin-kernel",
+      "version": "0.5.1",
+      "packageVersion": "0.5.13",
       "requires": [],
       "presentation": {
         "categoryOrder": 30,
-        "order": 30,
-        "description": "The Console lists the commands run in a project — the Agent's, from its own reports, and yours — with how each ended, how long it took and what it printed. You can run a command in the project folder yourself, run one again or stop it. It runs only for the person at this machine.",
+        "order": 25,
+        "description": "A live R session and a live Python session for each project, on this machine or on one of your servers. The Agent runs code in them to look at data and try things, and so can you: each cell keeps its code, what it printed, its plots and who ran it, and the session's variables stay between cells. You can interrupt a cell or stop a session; the next cell starts a new one.",
         "icon": {
-          "background": "#E8ECEF",
-          "color": "#3E4C57",
+          "background": "#E9EEF6",
+          "color": "#33507A",
           "paths": [
-            "M4.5 5.5h15a1 1 0 0 1 1 1v11a1 1 0 0 1-1 1h-15a1 1 0 0 1-1-1v-11a1 1 0 0 1 1-1z",
-            "m7.5 9.5 2.5 2.5-2.5 2.5",
-            "M12 14.5h4.5"
+            "M5 5.5h14a1 1 0 0 1 1 1v11a1 1 0 0 1-1 1H5a1 1 0 0 1-1-1v-11a1 1 0 0 1 1-1z",
+            "M8 9.5h3",
+            "M8 12h6",
+            "M8 14.5h4.5",
+            "M16.5 9.25v1.5"
           ]
         },
         "dependencies": [],
@@ -1093,82 +2053,601 @@
         "links": [
           {
             "label": "Source",
-            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/console"
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/kernel"
           },
           {
             "label": "Privacy",
             "url": "https://github.com/YuLab-SMU/Rho-plugins/blob/main/PRIVACY.md"
           }
         ],
-        "displayName": "Console",
-        "tagline": "Every command run in the project, and yours",
+        "displayName": "Notebook",
+        "tagline": "Live R and Python the Agent and you share",
         "category": "Working with your Agent",
         "examplePrompts": [
-          "“Run the analysis script again and show me what it printed.”",
-          "“Which command wrote results/summary.csv?”",
-          "“Why did the last command fail?”"
+          "“Load the table in the R session and show me its columns.”",
+          "“Fit the model in the session and keep it, so I can look at it.”",
+          "“Which variables are in the Python session now?”",
+          "“Run R on the lab server, in ~/projects/rnaseq, and load the counts there.”"
         ],
         "viewNote": "Its own page in each project",
         "readOnly": false,
         "runsCode": true
       },
       "listing": {
-        "actions": [
+        "operations": [
           {
+            "method": "kernel.run",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
             "presentation": {
               "order": 10,
-              "displayName": "Run a command",
-              "description": "Runs a command you typed in the project folder and keeps what it prints.",
+              "displayName": "Run a cell",
+              "description": "Runs code in the project's live R or Python session and keeps what it prints, its plots and the session's variables.",
               "readOnly": false,
               "runsCode": true
             }
           },
           {
+            "method": "kernel.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 20,
-              "displayName": "List commands",
-              "description": "Lists the commands run here, newest first, with how each ended.",
+              "displayName": "Read the session",
+              "description": "Reads the sessions, their variables and the cells run in them.",
               "readOnly": true,
               "runsCode": false
             }
           },
           {
+            "method": "kernel.events",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 25,
               "displayName": "Read who ran what",
-              "description": "Lists the commands run here, newest first: who ran each, when, in which folder and how it ended.",
+              "description": "Lists the cells run in the sessions, newest first: who ran each, when, where and how it ended.",
               "readOnly": true,
               "runsCode": false
             }
           },
           {
+            "method": "kernel.plot",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
               "order": 30,
-              "displayName": "Read output",
-              "description": "Reads what a command printed, page by page.",
+              "displayName": "Read a plot",
+              "description": "Reads one plot a cell drew, as a PNG image.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.inspect",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 35,
+              "displayName": "Look at a value",
+              "description": "Describes one value of a live session: a table's rows and columns, a model's fit and coefficients, a list's parts, a vector's values, a function's code.",
               "readOnly": true,
               "runsCode": false
             }
           },
           {
+            "method": "kernel.interrupt",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
             "presentation": {
               "order": 40,
-              "displayName": "Stop a command",
-              "description": "Asks a running command and the processes it started to stop.",
+              "displayName": "Interrupt a cell",
+              "description": "Stops the cell that is running; the session and its variables stay.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.stop",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
+            "presentation": {
+              "order": 50,
+              "displayName": "Stop a session",
+              "description": "Ends a session; its variables are gone.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.places",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 60,
+              "displayName": "Read the places",
+              "description": "Reads the servers sessions can run on, where each language's next session starts, and the files copied from them.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.place.set",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
+            "presentation": {
+              "order": 62,
+              "displayName": "Name a place",
+              "description": "Names a folder on a server as a place sessions can run in, removes one, or chooses where R or Python runs next.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.place.check",
+            "version": "2.0",
+            "effect": "native",
+            "requires": [],
+            "presentation": {
+              "order": 64,
+              "displayName": "Check a place",
+              "description": "Connects to a place and reports its system, its folder, and R and Python there.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.place.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 66,
+              "displayName": "List files on a server",
+              "description": "Lists a folder within a place's folder on its server.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.place.copy",
+            "version": "2.0",
+            "effect": "file",
+            "requires": [],
+            "presentation": {
+              "order": 68,
+              "displayName": "Copy a file from a server",
+              "description": "Copies one file from a place's folder into the project, under remote/<place>/, with its size, time and digest.",
               "readOnly": false,
               "runsCode": false
             }
+          },
+          {
+            "method": "kernel.servers",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 70,
+              "displayName": "Read your servers",
+              "description": "Reads the servers you manage with serverctl and the skills bound to each.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "kernel.server.skill",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 72,
+              "displayName": "Read a server's skill",
+              "description": "Reads one skill bound to a server: how that server is used.",
+              "readOnly": true,
+              "runsCode": false
+            }
           }
         ],
+        "actions": [],
+        "views": [
+          {
+            "id": "rho.notebook",
+            "version": "1",
+            "ui": "./ui",
+            "bindings": {},
+            "presentation": {
+              "displayName": "Notebook",
+              "description": "The cells run in the live R and Python sessions, with who ran each and why, what it printed and its plots, and a line to run your own.",
+              "readOnly": false,
+              "runsCode": true
+            }
+          },
+          {
+            "id": "rho.variables",
+            "version": "1",
+            "ui": "./ui",
+            "bindings": {},
+            "presentation": {
+              "displayName": "Variables",
+              "description": "The values each live session holds now.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "id": "rho.plots",
+            "version": "1",
+            "ui": "./ui",
+            "bindings": {},
+            "presentation": {
+              "displayName": "Plots",
+              "description": "The plots cells drew, newest first.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "id": "rho.flow",
+            "version": "1",
+            "ui": "./ui",
+            "bindings": {},
+            "presentation": {
+              "displayName": "Data flow",
+              "description": "How the values of the sessions were made: which cells read and defined each, and the files they named.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "id": "rho.servers",
+            "version": "1",
+            "ui": "./ui",
+            "bindings": {},
+            "presentation": {
+              "displayName": "Servers",
+              "description": "The servers sessions can run on, where each language runs, their files and the skills bound to them.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "id": "rho.object",
+            "version": "1",
+            "ui": "./ui",
+            "bindings": {},
+            "presentation": {
+              "displayName": "Value",
+              "description": "One value of a live session: a table's rows and columns, a model's fit, a list's parts.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          }
+        ],
+        "skills": [
+          {
+            "id": "kernel.session",
+            "version": "1.0",
+            "digest": "981c37eb09b5b31c091820c29e31d62d5b4303b5aa6fceaf407eb04fec5e8dff",
+            "presentation": {
+              "displayName": "Live session",
+              "description": "Explains how to run code in the project's live R and Python sessions."
+            },
+            "intent": "Run code in the live session and read what it printed.",
+            "requires": [
+              "kernel.run",
+              "kernel.read"
+            ],
+            "example": {
+              "method": "kernel.run",
+              "input": {
+                "language": "r",
+                "code": "summary(cars)",
+                "purpose": "Summarise the cars data",
+                "changeId": "cell-1",
+                "waitMs": 30000
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "limit",
+                "message": "Too many cells are waiting.",
+                "next": "Wait for the running cell, or interrupt it, then run again with a new changeId."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:notebook",
+              "description": "Runs R and Python cells, keeps their output, plots and variables, interrupts and stops sessions, and keeps identity across a restart."
+            }
+          }
+        ]
+      }
+    },
+    {
+      "id": "figures",
+      "package": "@rho-workspace/plugin-figures",
+      "version": "0.5.1",
+      "packageVersion": "0.5.1",
+      "requires": [
+        "kernel"
+      ],
+      "presentation": {
+        "categoryOrder": 20,
+        "order": 15,
+        "description": "A ggplot drawn in the project's live R session, by you or the Agent, is kept with every point, bar, box, line and label bound to the row of data it was drawn from. It works for any plot built on ggplot2 (ggtree, enrichplot, Seurat, patchwork and the rest) with no setup. Point at a mark to read its row, select marks by clicking or dragging, and ask the Agent about them: your message carries the exact rows. The Agent reads what a plot actually drew and can mark points for you with a note.",
+        "icon": {
+          "background": "#E8F2EE",
+          "color": "#2F6B57",
+          "paths": [
+            "M4.5 19.5h15",
+            "M4.5 19.5v-15",
+            "M8 15.5a1.25 1.25 0 1 0 0-.01",
+            "M12 10.5a1.25 1.25 0 1 0 0-.01",
+            "M16.5 13a1.25 1.25 0 1 0 0-.01",
+            "M14.5 6.5h5v5h-5z"
+          ]
+        },
+        "dependencies": [
+          {
+            "pluginId": "kernel",
+            "purpose": "to describe the plots its live R session draws"
+          }
+        ],
+        "developer": "Rho",
+        "license": "AGPL-3.0-only",
+        "links": [
+          {
+            "label": "Source",
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/figures"
+          },
+          {
+            "label": "Privacy",
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/blob/main/PRIVACY.md"
+          }
+        ],
+        "displayName": "Figures",
+        "tagline": "Plots whose marks know their data",
+        "category": "Figures & media",
+        "examplePrompts": [
+          "“Draw the volcano plot in the notebook; I will select the genes I care about.”",
+          "“What do the points I selected have in common?”",
+          "“Mark the genes in this plot with padj below 0.01 and say why they stand out.”",
+          "“Did the last plot drop any rows? Check what it actually drew.”"
+        ],
+        "viewNote": "In the Notebook and Plots, on every ggplot",
+        "readOnly": false,
+        "runsCode": false
+      },
+      "listing": {
+        "operations": [
+          {
+            "method": "figure.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 10,
+              "displayName": "Read a figure",
+              "description": "Reads what a plot drew: its layers, mappings, panels and data, the rows behind marks, and the marks people selected.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "figure.select",
+            "version": "2.0",
+            "effect": "metadata",
+            "requires": [],
+            "presentation": {
+              "order": 20,
+              "displayName": "Mark points in a figure",
+              "description": "Keeps a set of marks with a note, shown highlighted in the plot. It changes neither the plot nor its data.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          }
+        ],
+        "actions": [],
         "views": [],
         "skills": [
           {
-            "id": "console.workspace",
+            "id": "figures.read",
             "version": "1.0",
-            "digest": "519f869fbf9a1384f0d592ecf5db93c16516f96b90b95304646dd6d9b8798b59",
+            "digest": "63ce221852d48a6a7567710e37d18c18ffcad929ada2fc764d92b0b02bda1ad7",
+            "presentation": {
+              "displayName": "Figures",
+              "description": "Teaches the Agent to read what a plot drew, the rows behind its marks and the person's selections, and to point at marks."
+            },
+            "intent": "Read what a plot drew and the rows behind its marks, and point the person at marks.",
+            "requires": [
+              "figure.read",
+              "figure.select"
+            ],
+            "example": {
+              "method": "figure.read",
+              "input": {
+                "cellId": "k-0123456789abcdef",
+                "plot": 1,
+                "where": [
+                  {
+                    "column": "padj",
+                    "op": "lt",
+                    "value": 0.01
+                  }
+                ],
+                "limit": 20
+              }
+            },
+            "failureRecipes": [
+              {
+                "kind": "not_found",
+                "message": "This plot is a picture only: nothing described what it draws.",
+                "next": "Only ggplot2, base graphics and ComplexHeatmap pages, and matplotlib figures, drawn in a Notebook cell are described. Draw it with one of them to make its marks selectable, or read the picture with kernel.plot."
+              },
+              {
+                "kind": "not_found",
+                "message": "No Notebook cell saved a figure as this file with these bytes: it is a picture only.",
+                "next": "Save the plot in a Notebook cell (kernel.run): ggsave(), png() or pdf() and dev.off() in R, savefig() in Python. A file written by a script outside the live session is not described, nor a PDF of several pages."
+              },
+              {
+                "kind": "invalid",
+                "message": "A mark names no layer or row of this figure.",
+                "next": "Read the summary first; marks are \"layer.row\" counted from 0 within this figure."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:figures",
+              "description": "Describes real ggplot2, ggtree, Seurat-style and patchwork plots in R, and matplotlib and seaborn figures in Python, and reads, matches and selects their marks."
+            }
+          }
+        ]
+      }
+    },
+    {
+      "id": "skills",
+      "package": "@rho-workspace/plugin-skills",
+      "version": "0.1.0",
+      "packageVersion": "0.1.0",
+      "requires": [],
+      "presentation": {
+        "categoryOrder": 30,
+        "order": 28,
+        "description": "Skills are how work is done in this project: the methods you chose, the conventions you keep and the traps its work ran into, kept as SKILL.md files that every Agent here reads. Your Agent records what you decide and what it learns; each change says who made it, why and from what, and you can undo it.",
+        "icon": {
+          "background": "#EEF0E4",
+          "color": "#4F5A2E",
+          "paths": [
+            "M6.5 4.5h10a1.5 1.5 0 0 1 1.5 1.5v13.5h-10A1.5 1.5 0 0 1 6.5 18z",
+            "M6.5 18a1.5 1.5 0 0 1 1.5-1.5h10",
+            "M10 8.5h4.5",
+            "M10 11.5h3"
+          ]
+        },
+        "dependencies": [],
+        "developer": "Rho",
+        "license": "AGPL-3.0-only",
+        "links": [
+          {
+            "label": "Source",
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/tree/main/plugins/skills"
+          },
+          {
+            "label": "Privacy",
+            "url": "https://github.com/YuLab-SMU/Rho-plugins/blob/main/PRIVACY.md"
+          }
+        ],
+        "displayName": "Skills",
+        "tagline": "How work is done here, kept by your Agent and you",
+        "category": "Working with your Agent",
+        "examplePrompts": [
+          "“For this project we report proportions as percentages.”",
+          "“What have you learned about how this project is done?”",
+          "“Undo what you recorded about the frequency fits.”"
+        ],
+        "viewNote": "Its own page in each project",
+        "readOnly": false,
+        "runsCode": false
+      },
+      "listing": {
+        "operations": [
+          {
+            "method": "skills.list",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
             "presentation": {
-              "displayName": "Console",
-              "description": "Explains what the console records and that it runs commands only for the person."
+              "order": 10,
+              "displayName": "List skills",
+              "description": "Lists the project's skills, what each is for and its newest change.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "skills.read",
+            "version": "2.0",
+            "effect": "read",
+            "requires": [],
+            "presentation": {
+              "order": 20,
+              "displayName": "Read a skill",
+              "description": "Reads one skill and its changes, each with who made it, why and from what.",
+              "readOnly": true,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "skills.change",
+            "version": "2.0",
+            "effect": "file",
+            "requires": [],
+            "presentation": {
+              "order": 30,
+              "displayName": "Record in a skill",
+              "description": "Writes a skill in the project: a new one, a change with its reason and evidence, or its removal.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          },
+          {
+            "method": "skills.undo",
+            "version": "2.0",
+            "effect": "file",
+            "requires": [],
+            "presentation": {
+              "order": 40,
+              "displayName": "Undo a change",
+              "description": "Puts a skill back as it was before its newest change.",
+              "readOnly": false,
+              "runsCode": false
+            }
+          }
+        ],
+        "actions": [],
+        "views": [],
+        "skills": [
+          {
+            "id": "skills.project",
+            "version": "1.0",
+            "digest": "114a4c98e98625c98385da800112f9533fc7d43a078fa0e40d6a4a3641fb27e5",
+            "presentation": {
+              "displayName": "Project skills",
+              "description": "How to read the project's skills before working and record what the person decides and what the work teaches."
+            },
+            "intent": "Follow how this project is done, and keep it as the person decides and the work teaches.",
+            "requires": [
+              "skills.list",
+              "skills.read",
+              "skills.change"
+            ],
+            "example": {
+              "method": "skills.list",
+              "input": {}
+            },
+            "failureRecipes": [
+              {
+                "kind": "conflict",
+                "message": "The skill changed since that version.",
+                "next": "Read it again with skills.read and make the change on its current version."
+              },
+              {
+                "kind": "limit",
+                "message": "The skill would be larger than a project skill holds.",
+                "next": "Shorten it: merge entries and drop those that no longer apply, then change it again."
+              }
+            ],
+            "verify": {
+              "command": "npm run test:skills",
+              "description": "Creates, changes, undoes and removes project skills, sees a change made outside Rho, and keeps each change's author, reason and evidence."
             }
           }
         ]