diff --git a/packages/core/src/tool.ts b/packages/core/src/tool.ts
index 88634be3e09..2f6294ceb10 100644
--- a/packages/core/src/tool.ts
+++ b/packages/core/src/tool.ts
@@ -4,7 +4,7 @@ export type { Context, Metadata, Options, Result } from "@opencode-ai/schema/too
 
 import { ToolDefinition, type ToolCall } from "@opencode-ai/ai"
 import { Tool } from "@opencode-ai/schema/tool"
-import { Context, Effect, Layer, Result, Schema, SchemaIssue } from "effect"
+import { Context, Effect, Layer, Result, Schema, SchemaIssue, Types } from "effect"
 import { makeLocationNode } from "@opencode-ai/util/effect/app-node"
 import type { Agent } from "./agent.js"
 import { CodeModeCatalog } from "./codemode/catalog.js"
@@ -25,6 +25,8 @@ export class RegistrationError extends Schema.TaggedError<RegistrationError>()("
 
 export interface Draft {
   readonly add: (tool: Tool.Info) => void
+  readonly update: (id: string, update: (tool: Types.Mutable<Tool.Info>) => void) => void
+  readonly remove: (id: string) => void
 }
 
 type Data = {
@@ -156,6 +158,24 @@ const layer = Layer.effect(
           }
           draft.tools.set(effectiveName(tool), { ...tool, options: tool.options && { ...tool.options } })
         },
+        update: (id, update) => {
+          const current = draft.tools.get(id)
+          if (!current) return
+          const tool = { ...current, options: current.options && { ...current.options } }
+          update(tool)
+          tool.name = current.name
+          if (tool.options?.namespace !== current.options?.namespace)
+            tool.options = { ...tool.options, namespace: current.options?.namespace }
+          const error = registrationError(tool)
+          if (error) {
+            draft.errors.push({ tool, error })
+            return
+          }
+          draft.tools.set(id, tool)
+        },
+        remove: (id) => {
+          draft.tools.delete(id)
+        },
       }),
       finalize: () =>
         Effect.forEach(
diff --git a/packages/core/src/tool/AGENTS.md b/packages/core/src/tool/AGENTS.md
index 2c9c9263274..e10969412af 100644
--- a/packages/core/src/tool/AGENTS.md
+++ b/packages/core/src/tool/AGENTS.md
@@ -30,11 +30,12 @@ Leaves own resolution, permission, and side-effect ordering. Translate only expe
 
 ## Registration
 
-Built-ins, plugins, and MCP install tools through `Tool.Service.transform`, adding complete tool objects to the add-only draft. A tool may provide a namespace, which flattens direct model names to `<namespace>_<tool>`, and defaults into CodeMode (`codemode` defaults true; `codemode: false` keeps the tool on the provider's native tool list).
+Built-ins, plugins, and MCP install tools through `Tool.Service.transform`, adding complete tool objects to the draft. A tool may provide a namespace, which flattens direct model names to `<namespace>_<tool>`, and defaults into CodeMode (`codemode` defaults true; `codemode: false` keeps the tool on the provider's native tool list).
 
 The service uses shared `State` to replay synchronous transforms in registration order against a fresh draft. `Tool.Service.reload()` rebuilds from captured source data without changing registration precedence. Registrations are scoped and return a real, idempotent `dispose` Effect:
 
 - The latest valid active registration for the same effective name wins.
+- `update` and `remove` target effective names and do nothing for missing tools. Updates preserve the name and namespace; invalid updates leave the previous definition intact. Creating a tool requires `add`.
 - Disposing a registration or closing its scope removes only its transform and rebuilds from the remaining transforms, revealing any earlier definition it overrode.
 - Each model request captures the effective definitions and executors it advertises; later reloads and disposal affect later snapshots. Captured executors may still reference mutable producer-owned state.
 
diff --git a/packages/core/test/mcp.test.ts b/packages/core/test/mcp.test.ts
index 970aeff119e..d4236ea42ca 100644
--- a/packages/core/test/mcp.test.ts
+++ b/packages/core/test/mcp.test.ts
@@ -1282,7 +1282,7 @@ test("serializes concurrent MCP lifecycle operations", async () => {
   )
 })
 
-testEffect(Layer.empty).live("isolates invalid MCP tools and preserves overrides through catalog updates", () =>
+testEffect(Layer.empty).live("isolates invalid MCP tools and preserves plugin transforms through catalog updates", () =>
   Effect.gen(function* () {
     const tool = (server: string, name: string, description = name) =>
       new MCP.Tool({
@@ -1316,6 +1316,12 @@ testEffect(Layer.empty).live("isolates invalid MCP tools and preserves overrides
           execute: () => Effect.succeed({ output: "override" }),
         })
       })
+      const mutation = yield* registry.transform((draft) => {
+        draft.update("other_lookup", (tool) => {
+          tool.description += " updated"
+        })
+        draft.remove("repaired_lookup")
+      })
 
       yield* Ref.set(catalog, [tool("demo", "y".repeat(65)), ...healthy, tool("demo", "added"), namespace])
       yield* bus.publish(McpEvent.ToolsChanged, { server: "demo" })
@@ -1329,6 +1335,9 @@ testEffect(Layer.empty).live("isolates invalid MCP tools and preserves overrides
       expect((yield* toolDefinitions(registry)).find((tool) => tool.name === "demo_search")?.description).toBe(
         "Override search",
       )
+      expect((yield* toolDefinitions(registry)).find((tool) => tool.name === "other_lookup")?.description).toBe(
+        "lookup updated",
+      )
       yield* Effect.forEach(["demo_search", "other_lookup"], (name) =>
         executeTool(registry, {
           sessionID: Session.ID.make("ses_mcp_invalid_catalog"),
@@ -1359,12 +1368,19 @@ testEffect(Layer.empty).live("isolates invalid MCP tools and preserves overrides
         "demo_search",
         "demo_status",
         "other_lookup",
-        "repaired_lookup",
         "execute",
       ])
       expect((yield* toolDefinitions(registry)).find((tool) => tool.name === "demo_search")?.description).toBe(
         "Override search",
       )
+      expect((yield* toolDefinitions(registry)).find((tool) => tool.name === "other_lookup")?.description).toBe(
+        "lookup updated",
+      )
+      yield* mutation.dispose
+      expect((yield* toolDefinitions(registry)).map((tool) => tool.name)).toContain("repaired_lookup")
+      expect((yield* toolDefinitions(registry)).find((tool) => tool.name === "other_lookup")?.description).toBe(
+        "lookup",
+      )
 
       yield* Ref.set(catalog, [tool("demo", "search", "Latest search"), tool("demo", "refreshed")])
       yield* bus.publish(McpEvent.ToolsChanged, { server: "demo" })
diff --git a/packages/core/test/plugin/promise.test.ts b/packages/core/test/plugin/promise.test.ts
index 875e7e64143..756fada4264 100644
--- a/packages/core/test/plugin/promise.test.ts
+++ b/packages/core/test/plugin/promise.test.ts
@@ -694,6 +694,86 @@ describe("fromPromise", () => {
     }),
   )
 
+  it.live("adapts tool updates, executor wrapping, and removal across replay and disposal", () =>
+    Effect.gen(function* () {
+      const plugins = yield* Plugin.Service
+      const registry = yield* Tool.Service
+      const host = yield* PluginHost.make(plugins)
+      const progress: Tool.Metadata[] = []
+      let greeting = "Hello"
+      const registrations: Array<{ dispose: () => Promise<void> }> = []
+      yield* host.tool.transform((draft) => {
+        const text = greeting
+        draft.add({
+          name: "hello",
+          description: "Hello",
+          options: { namespace: "acme", codemode: false },
+          input: Schema.Struct({ name: Schema.String }),
+          output: Schema.String,
+          execute: ({ name }, context) =>
+            context.progress({ phase: "original" }).pipe(Effect.as({ output: `${text}, ${name}!` })),
+        })
+        draft.add({
+          name: "temporary",
+          description: "Temporary",
+          input: Schema.Struct({}),
+          options: { codemode: false },
+          execute: () => Effect.succeed({ content: "temporary" }),
+        })
+      })
+      yield* PluginPromise.fromPromise(
+        define({
+          id: "promise-tool-mutations",
+          setup: async (ctx) => {
+            registrations.push(
+              await ctx.tool.transform((draft) => {
+                draft.update("missing", () => {
+                  throw new Error("must not create a tool")
+                })
+                draft.update("acme_hello", (tool) => {
+                  const execute = tool.execute
+                  tool.description = "Wrapped"
+                  delete tool.output
+                  tool.execute = async (input, context) => {
+                    const result = await execute(input, context)
+                    return { content: `${result.output} Wrapped.` }
+                  }
+                })
+                draft.remove("temporary")
+              }),
+            )
+            greeting = "Hi"
+            await ctx.tool.reload()
+          },
+        }),
+      ).effect(host)
+      const snapshot = yield* registry.snapshot()
+      expect(snapshot.definitions.map((tool) => tool.name)).toEqual(["acme_hello", "execute"])
+      expect(snapshot.definitions[0]?.description).toBe("Wrapped")
+      expect(snapshot.definitions[0]?.outputSchema).toBeUndefined()
+      expect(
+        yield* snapshot.execute({
+          sessionID: Session.ID.make("ses_promise_tool_update"),
+          agent: Agent.ID.make("build"),
+          messageID: SessionMessage.ID.make("msg_promise_tool_update"),
+          call: { type: "tool-call", id: "call_update", name: "acme_hello", input: { name: "world" } },
+          progress: (update) =>
+            Effect.sync(() => {
+              progress.push(update)
+            }),
+        }),
+      ).toMatchObject({ content: [{ type: "text", text: "Hi, world! Wrapped." }] })
+      expect(progress).toEqual([{ phase: "original" }])
+      const registration = registrations[0]
+      if (!registration) return yield* Effect.die("Promise tool registration was not captured")
+      yield* Effect.promise(() => registration.dispose())
+      yield* Effect.promise(() => registration.dispose())
+      const restored = yield* registry.snapshot()
+      expect(restored.definitions.map((tool) => tool.name)).toEqual(["acme_hello", "temporary", "execute"])
+      expect(restored.definitions[0]?.description).toBe("Hello")
+    }),
+  )
+
   it.effect("returns content-only plugin results through Code Mode", () =>
     Effect.gen(function* () {
       const plugins = yield* Plugin.Service
diff --git a/packages/core/test/session-runner-tool-registry.test.ts b/packages/core/test/session-runner-tool-registry.test.ts
index b651686bcf3..696e86e0e6f 100644
--- a/packages/core/test/session-runner-tool-registry.test.ts
+++ b/packages/core/test/session-runner-tool-registry.test.ts
@@ -73,6 +73,115 @@ const transform = (service: Tool.Interface, tools: Readonly<Record<string, Info>
   )
 
 describe("Tool", () => {
+  it.effect("replays mutations on refreshed sources and restores tools on disposal and scope cleanup", () =>
+    Effect.gen(function* () {
+      const service = yield* Tool.Service
+      let text = "original"
+      const source = yield* Scope.make()
+      yield* service
+        .transform((draft) => {
+          draft.add({ ...constant(text), name: "echo", options: { namespace: "acme", codemode: false } })
+          draft.add({ ...make(), name: "hidden" })
+        })
+        .pipe(Scope.provide(source))
+      const original = yield* service.snapshot()
+      const update = yield* service.transform((draft) => {
+        draft.update("missing", () => {
+          throw new Error("must not create a tool")
+        })
+        draft.remove("missing")
+        draft.update("acme_echo", (tool) => {
+          const execute = tool.execute
+          tool.description = "Updated"
+          tool.execute = (input, context) =>
+            execute(input, context).pipe(
+              Effect.map((result) => ({ ...result, output: { text: `${result.output.text} updated` } })),
+            )
+        })
+      })
+      const scope = yield* Scope.make()
+      yield* service.transform((draft) => draft.remove("hidden")).pipe(Scope.provide(scope))
+      expect((yield* service.snapshot()).codeModeCatalog).toEqual([])
+      expect((yield* executeTool(service, call("acme_echo"))).output).toEqual({ text: "original updated" })
+
+      text = "refreshed"
+      const reload = yield* service.reload().pipe(Effect.forkChild({ startImmediately: true }))
+      yield* TestClock.adjust("500 millis")
+      yield* Fiber.join(reload)
+      const refreshed = yield* service.snapshot()
+      expect(refreshed.definitions[0]?.description).toBe("Updated")
+      expect(refreshed.codeModeCatalog).toEqual([])
+      expect((yield* refreshed.execute(call("acme_echo"))).output).toEqual({ text: "refreshed updated" })
+      expect((yield* original.execute(call("acme_echo"))).output).toEqual({ text: "original" })
+
+      yield* update.dispose
+      yield* update.dispose
+      expect((yield* executeTool(service, call("acme_echo"))).output).toEqual({ text: "refreshed" })
+      yield* Scope.close(scope, Exit.void)
+      expect((yield* service.snapshot()).codeModeCatalog?.map((tool) => tool.path)).toEqual(["hidden"])
+
+      yield* service.transform((draft) =>
+        draft.update("acme_echo", (tool) => {
+          tool.description = "Updated again"
+        }),
+      )
+      yield* Scope.close(source, Exit.void)
+      expect((yield* service.snapshot()).definitions.map((tool) => tool.name)).toEqual(["execute"])
+    }),
+  )
+
+  it.effect("updates schemas and executors without renaming tools and applies removal in order", () =>
+    Effect.gen(function* () {
+      const service = yield* Tool.Service
+      yield* service.transform((draft) => {
+        draft.add({ ...make(), options: { namespace: "acme.tools", codemode: false } })
+        draft.add({ ...make(), name: "removed", options: { codemode: false } })
+        draft.remove("removed")
+        draft.update("removed", () => {
+          throw new Error("must not resurrect a tool")
+        })
+        draft.remove("acme_tools_echo")
+        draft.add({ ...make(), options: { namespace: "acme.tools", codemode: false } })
+        draft.update("acme_tools_echo", (tool) => {
+          tool.name = "renamed"
+          tool.options = { namespace: "other", codemode: false }
+          tool.input = Schema.Struct({ value: Schema.Finite })
+          tool.output = Schema.Finite
+          tool.execute = ({ value }) => Effect.succeed({ output: value + 1 })
+        })
+      })
+      const snapshot = yield* service.snapshot()
+      expect(snapshot.definitions.map((tool) => tool.name)).toEqual(["acme_tools_echo", "execute"])
+      expect(snapshot.definitions[0]?.inputSchema.properties).toEqual({ value: { type: "number" } })
+      expect(
+        (yield* snapshot.execute({
+          ...call("acme_tools_echo"),
+          call: {
+            type: "tool-call",
+            id: "updated",
+            name: "acme_tools_echo",
+            input: { value: 2 },
+          },
+        })).output,
+      ).toBe(3)
+      expect(yield* snapshot.execute(call("acme_tools_echo")).pipe(Effect.flip)).toBeInstanceOf(Tool.Error)
+    }),
+  )
+
+  it.effect("skips invalid updates without dropping the existing definition", () =>
+    Effect.gen(function* () {
+      const service = yield* Tool.Service
+      yield* transform(service, { echo: make() }, { codemode: false })
+      yield* service.transform((draft) =>
+        draft.update("echo", (tool) => {
+          Object.assign(tool, { description: undefined })
+        }),
+      )
+      expect((yield* service.snapshot()).definitions[0]?.description).toBe("Echo text")
+      expect((yield* executeTool(service, call("echo"))).output).toEqual({ text: "echo" })
+    }),
+  )
+
   it.effect("replays empty sources on reload and keeps advertised snapshots", () =>
     Effect.gen(function* () {
       const service = yield* Tool.Service
diff --git a/packages/plugin/src/effect/tool.ts b/packages/plugin/src/effect/tool.ts
index a87250a6339..3411955e798 100644
--- a/packages/plugin/src/effect/tool.ts
+++ b/packages/plugin/src/effect/tool.ts
@@ -2,13 +2,16 @@ import { Tool } from "@opencode-ai/schema/tool"
 import type { Agent } from "@opencode-ai/schema/agent"
 import type { Session } from "@opencode-ai/schema/session"
 import type { SessionMessage } from "@opencode-ai/schema/session-message"
-import type { Effect, JsonSchema } from "effect"
+import type { Effect, JsonSchema, Types } from "effect"
 import type { Hooks, Transform } from "./registration.js"
 
 export interface ToolDraft {
   add<Input extends Tool.ValueSchema<any>, Output extends Tool.ValueSchema<any> | undefined>(
     tool: Tool.Info<Input, Output>,
   ): void
+  /** Updates an existing tool; missing IDs are ignored. */
+  update(id: string, update: (tool: Types.Mutable<Tool.Info>) => void): void
+  remove(id: string): void
 }
 
 export interface ToolHooks {
diff --git a/packages/plugin/src/promise/adapter.ts b/packages/plugin/src/promise/adapter.ts
index 6ad5bf3fca5..f88d8f68506 100644
--- a/packages/plugin/src/promise/adapter.ts
+++ b/packages/plugin/src/promise/adapter.ts
@@ -301,6 +301,28 @@ export function fromPromise(plugin: Plugin) {
                         ...tool,
                         execute: (input, context) => executePromiseTool(tool, input, context),
                       }),
+                    update: (id, update) =>
+                      draft.update(id, (tool) => {
+                        const execute = tool.execute
+                        const value: Info = {
+                          ...tool,
+                          execute: (input, context) =>
+                            run(
+                              execute(input, {
+                                ...context,
+                                progress: (update) => Effect.promise(() => context.progress(update)),
+                              }),
+                            ),
+                        }
+                        update(value)
+                        Object.assign(tool, value, {
+                          output: value.output,
+                          options: value.options,
+                          execute: (input: Parameters<Info["execute"]>[0], context: Tool.Context) =>
+                            executePromiseTool(value, input, context),
+                        })
+                      }),
+                    remove: draft.remove,
                   }),
                 ),
               ),
diff --git a/packages/plugin/src/promise/tool.ts b/packages/plugin/src/promise/tool.ts
index c1464beb464..764feab9ded 100644
--- a/packages/plugin/src/promise/tool.ts
+++ b/packages/plugin/src/promise/tool.ts
@@ -5,7 +5,7 @@ import { Tool } from "@opencode-ai/schema/tool"
 import type { Agent } from "@opencode-ai/schema/agent"
 import type { Session } from "@opencode-ai/schema/session"
 import type { SessionMessage } from "@opencode-ai/schema/session-message"
-import type { JsonSchema } from "effect"
+import type { JsonSchema, Types } from "effect"
 import type { Hooks, Transform } from "./registration.js"
 
 export interface ToolContext extends Omit<Tool.Context, "progress"> {
@@ -26,6 +26,9 @@ interface ToolDraft {
   add<Input extends Tool.ValueSchema<any>, Output extends Tool.ValueSchema<any> | undefined>(
     tool: Info<Input, Output>,
   ): void
+  /** Updates an existing tool; missing IDs are ignored. */
+  update(id: string, update: (tool: Types.Mutable<Info>) => void): void
+  remove(id: string): void
 }
 
 interface ToolHooks {
diff --git a/packages/www/src/docs/content/build/plugins/effect.mdx b/packages/www/src/docs/content/build/plugins/effect.mdx
index 2bd64985966..7e3eac46dec 100644
--- a/packages/www/src/docs/content/build/plugins/effect.mdx
+++ b/packages/www/src/docs/content/build/plugins/effect.mdx
@@ -829,7 +829,7 @@ interface StorageDomain {
 Register typed tools with Effect `Schema`. The executor receives decoded input and returns an Effect containing typed
 output, display content, or metadata.
 
-The draft is add-only and the transform callback is synchronous: it must not return an Effect or Promise. Load
+The draft supports `add`, `update`, and `remove`. The transform callback is synchronous: it must not return an Effect or Promise. Load
 external data before registering or reloading. OpenCode replays active transforms in registration order on a fresh
 draft; for the same effective tool name, a later valid registration overrides an earlier one.
 
@@ -857,6 +857,22 @@ effect: (ctx) =>
 Call `yield* ctx.tool.reload()` after changing source data captured by the callback. Reload replays active transforms
 without changing their order; it does not rerun the plugin effect.
 
+`update` and `remove` target the effective tool name, including its namespace (`acme_greeting` above). Dots in
+namespaces and unsupported characters in tool names become `_`. Missing names are ignored; creating a tool requires
+`add` with a complete definition. Updates preserve the name and namespace. Assign new schemas or options to replace
+them rather than mutating nested values. Invalid updates are logged and leave the previous definition intact.
+
+```ts
+yield* ctx.tool.transform((draft) => {
+  draft.update("acme_greeting", (tool) => {
+    tool.description = "Greet the user by name"
+  })
+  draft.remove("acme_obsolete")
+})
+```
+
+Updates and removals replay in order with additions, including after MCP catalog refreshes.
+
 `transform` returns a scoped registration. Run `yield* registration.dispose` to remove its transform and rebuild
 from the remaining transforms, revealing any earlier definition it overrode. Disposal is idempotent, and closing
 the plugin scope also disposes its registrations.
@@ -873,6 +889,8 @@ interface ToolDraft {
   add<Input extends Tool.ValueSchema<any>, Output extends Tool.ValueSchema<any> | undefined>(
     tool: Tool.Info<Input, Output>,
   ): void
+  update(id: string, update: (tool: Types.Mutable<Tool.Info>) => void): void
+  remove(id: string): void
 }
 
 interface ToolDomain {
diff --git a/packages/www/src/docs/content/build/plugins/index.mdx b/packages/www/src/docs/content/build/plugins/index.mdx
index 184322961c6..e9ff114e83f 100644
--- a/packages/www/src/docs/content/build/plugins/index.mdx
+++ b/packages/www/src/docs/content/build/plugins/index.mdx
@@ -784,7 +784,7 @@ interface StorageScanResult {
 
 ### Tools
 
-Register tools with an add-only transform. The callback is synchronous, including in Promise plugins; load external
+Register, update, and remove tools with a transform. The callback is synchronous, including in Promise plugins; load external
 data before registering or reloading. OpenCode replays active transforms in registration order on a fresh draft.
 For the same effective tool name, a later valid registration overrides an earlier one.
 
@@ -815,6 +815,23 @@ changing their order; it does not rerun plugin setup.
 await ctx.tool.reload()
 ```
 
+Use `update` and `remove` with the effective tool name, including its namespace (`acme_greeting` above). Dots in
+namespaces and unsupported characters in tool names become `_`. Missing names are ignored; creating a tool requires
+`add` with a complete definition. Updates preserve the name and namespace. Assign new schemas or options to replace
+them rather than mutating nested values. Invalid updates are logged and leave the previous definition intact.
+
+```ts
+await ctx.tool.transform((draft) => {
+  draft.update("acme_greeting", (tool) => {
+    tool.description = "Greet the user by name"
+  })
+  draft.remove("acme_obsolete")
+})
+```
+
+Updates and removals replay in order with additions, including after MCP catalog refreshes. Disposing their
+registration removes those changes and rebuilds from the remaining transforms.
+
 Dispose a registration to remove its transform and rebuild from the remaining transforms, revealing any earlier
 definition it overrode. Disposal is idempotent, and unloading the plugin also disposes its registrations.
 
@@ -839,6 +856,8 @@ interface ToolContext {
 
 interface ToolDraft {
   add(tool: ToolInfo): void
+  update(id: string, update: (tool: Types.Mutable<ToolInfo>) => void): void
+  remove(id: string): void
 }
 ```