diff --git a/packages/core/src/mcp/guidance.ts b/packages/core/src/mcp/guidance.ts
index 8334e7b063..89882ea19b 100644
--- a/packages/core/src/mcp/guidance.ts
+++ b/packages/core/src/mcp/guidance.ts
@@ -14,16 +14,42 @@ const Summary = Schema.Struct({
 })
 type Summary = typeof Summary.Type
 
+const entries = (servers: ReadonlyArray<Summary>) =>
+  servers.flatMap((server) => [
+    `  <server name="${server.server}">`,
+    ...server.instructions.split("\n").map((line) => `    ${line}`),
+    "  </server>",
+  ])
+
 const render = (servers: ReadonlyArray<Summary>) =>
-  [
-    "<mcp_instructions>",
-    ...servers.flatMap((server) => [
-      `  <server name="${server.server}">`,
-      ...server.instructions.split("\n").map((line) => `    ${line}`),
-      "  </server>",
-    ]),
-    "</mcp_instructions>",
+  ["<mcp_instructions>", ...entries(servers), "</mcp_instructions>"].join("\n")
+
+const update = (previous: ReadonlyArray<Summary>, current: ReadonlyArray<Summary>) => {
+  const names = new Set(current.map((server) => server.server))
+  const previousByName = new Map(previous.map((server) => [server.server, server]))
+  const added = current.filter((server) => !previousByName.has(server.server))
+  const removed = previous.filter((server) => !names.has(server.server))
+  const changed = current.filter((server) => {
+    const before = previousByName.get(server.server)
+    return before !== undefined && before.instructions !== server.instructions
+  })
+  // Additions and removals render as small deltas; anything else restates the full list.
+  if (changed.length > 0 || (added.length === 0 && removed.length === 0))
+    return [
+      "The available MCP server instructions have changed. This list supersedes the previous one.",
+      render(current),
+    ].join("\n")
+  return [
+    ...(added.length === 0
+      ? []
+      : ["New MCP server instructions are available in addition to those previously listed:", ...entries(added)]),
+    ...(removed.length === 0
+      ? []
+      : [
+          `Instructions for the following MCP servers are no longer available: ${removed.map((server) => server.server).join(", ")}.`,
+        ]),
   ].join("\n")
+}
 
 export interface Interface {
   readonly load: (agent: AgentV2.Selection) => Effect.Effect<SystemContext.SystemContext>
@@ -50,7 +76,8 @@ export const layer = Layer.effect(
             return (
               owned.length === 0 ||
               owned.some(
-                (tool) => PermissionV2.evaluate(McpTool.name(tool.server, tool.name), "*", agent.permissions).effect !== "deny",
+                (tool) =>
+                  PermissionV2.evaluate(McpTool.name(tool.server, tool.name), "*", agent.permissions).effect !== "deny",
               )
             )
           })
@@ -61,11 +88,7 @@ export const layer = Layer.effect(
           codec: Schema.toCodecJson(Schema.Array(Summary)),
           load: Effect.succeed(visible),
           baseline: render,
-          update: (_previous, current) =>
-            [
-              "The available MCP server instructions have changed. This list supersedes the previous one.",
-              render(current),
-            ].join("\n"),
+          update,
           removed: () => "MCP server instructions are no longer available.",
         })
       }),
diff --git a/packages/core/src/reference/guidance.ts b/packages/core/src/reference/guidance.ts
index 11fcb9ecea..6544852df2 100644
--- a/packages/core/src/reference/guidance.ts
+++ b/packages/core/src/reference/guidance.ts
@@ -11,20 +11,50 @@ const Summary = Schema.Struct({
   description: Schema.String.pipe(Schema.optional),
 })
 
+const entries = (references: ReadonlyArray<typeof Summary.Type>) =>
+  references.flatMap((reference) => [
+    "  <reference>",
+    `    <name>${reference.name}</name>`,
+    `    <path>${reference.path}</path>`,
+    ...(reference.description === undefined ? [] : [`    <description>${reference.description}</description>`]),
+    "  </reference>",
+  ])
+
 const render = (references: ReadonlyArray<typeof Summary.Type>) =>
   [
     "Project references provide additional directories that can be accessed when relevant.",
     "<available_references>",
-    ...references.flatMap((reference) => [
-      "  <reference>",
-      `    <name>${reference.name}</name>`,
-      `    <path>${reference.path}</path>`,
-      ...(reference.description === undefined ? [] : [`    <description>${reference.description}</description>`]),
-      "  </reference>",
-    ]),
+    ...entries(references),
     "</available_references>",
   ].join("\n")
 
+const update = (previous: ReadonlyArray<typeof Summary.Type>, current: ReadonlyArray<typeof Summary.Type>) => {
+  const names = new Set(current.map((reference) => reference.name))
+  const previousByName = new Map(previous.map((reference) => [reference.name, reference]))
+  const added = current.filter((reference) => !previousByName.has(reference.name))
+  const removed = previous.filter((reference) => !names.has(reference.name))
+  const changed = current.filter((reference) => {
+    const before = previousByName.get(reference.name)
+    return before !== undefined && (before.path !== reference.path || before.description !== reference.description)
+  })
+  // Additions and removals render as small deltas; anything else restates the full list.
+  if (changed.length > 0 || (added.length === 0 && removed.length === 0))
+    return [
+      "The available project references have changed. This list supersedes the previous reference list.",
+      render(current),
+    ].join("\n")
+  return [
+    ...(added.length === 0
+      ? []
+      : ["New project references are available in addition to those previously listed:", ...entries(added)]),
+    ...(removed.length === 0
+      ? []
+      : [
+          `The following project references are no longer available and must not be used: ${removed.map((reference) => reference.name).join(", ")}.`,
+        ]),
+  ].join("\n")
+}
+
 export interface Interface {
   readonly load: () => Effect.Effect<SystemContext.SystemContext>
 }
@@ -52,11 +82,7 @@ const layer = Layer.effect(
           codec: Schema.toCodecJson(Schema.Array(Summary)),
           load: Effect.succeed(available),
           baseline: render,
-          update: (_previous, current) =>
-            [
-              "The available project references have changed. This list supersedes the previous reference list.",
-              render(current),
-            ].join("\n"),
+          update,
           removed: () => "Project reference guidance is no longer available. Do not use previously listed references.",
         })
       }),
diff --git a/packages/core/src/skill/guidance.ts b/packages/core/src/skill/guidance.ts
index f2ec815744..abca17b6b0 100644
--- a/packages/core/src/skill/guidance.ts
+++ b/packages/core/src/skill/guidance.ts
@@ -13,23 +13,49 @@ const Summary = Schema.Struct({
 })
 type Summary = typeof Summary.Type
 
+const entries = (skills: ReadonlyArray<Summary>) =>
+  skills.flatMap((skill) => [
+    "  <skill>",
+    `    <name>${skill.name}</name>`,
+    `    <description>${skill.description}</description>`,
+    "  </skill>",
+  ])
+
 const render = (skills: ReadonlyArray<Summary>) =>
   [
     "Skills provide specialized instructions and workflows for specific tasks.",
     "Use the skill tool to load a skill when a task matches its description.",
     ...(skills.length === 0
       ? ["No skills are currently available."]
+      : ["<available_skills>", ...entries(skills), "</available_skills>"]),
+  ].join("\n")
+
+const update = (previous: ReadonlyArray<Summary>, current: ReadonlyArray<Summary>) => {
+  const names = new Set(current.map((skill) => skill.name))
+  const previousByName = new Map(previous.map((skill) => [skill.name, skill]))
+  const added = current.filter((skill) => !previousByName.has(skill.name))
+  const removed = previous.filter((skill) => !names.has(skill.name))
+  const changed = current.filter((skill) => {
+    const before = previousByName.get(skill.name)
+    return before !== undefined && before.description !== skill.description
+  })
+  // Additions and removals render as small deltas; anything else restates the full list.
+  if (changed.length > 0 || (added.length === 0 && removed.length === 0))
+    return [
+      "The available skills have changed. This list supersedes the previous available skills list.",
+      render(current),
+    ].join("\n")
+  return [
+    ...(added.length === 0
+      ? []
+      : ["New skills are available in addition to those previously listed:", ...entries(added)]),
+    ...(removed.length === 0
+      ? []
       : [
-          "<available_skills>",
-          ...skills.flatMap((skill) => [
-            "  <skill>",
-            `    <name>${skill.name}</name>`,
-            `    <description>${skill.description}</description>`,
-            "  </skill>",
-          ]),
-          "</available_skills>",
+          `The following skills are no longer available and must not be used: ${removed.map((skill) => skill.name).join(", ")}.`,
         ]),
   ].join("\n")
+}
 
 export interface Interface {
   readonly load: (agent: AgentV2.Selection) => Effect.Effect<SystemContext.SystemContext>
@@ -61,11 +87,7 @@ const layer = Layer.effect(
           codec: Schema.toCodecJson(Schema.Array(Summary)),
           load: Effect.succeed(available),
           baseline: render,
-          update: (_previous, current) =>
-            [
-              "The available skills have changed. This list supersedes the previous available skills list.",
-              render(current),
-            ].join("\n"),
+          update,
           removed: () => "Skill guidance is no longer available. Do not use any previously listed skill.",
         })
       }),
diff --git a/packages/core/test/reference-guidance.test.ts b/packages/core/test/reference-guidance.test.ts
index 4ff4a2ace4..3db3212c3c 100644
--- a/packages/core/test/reference-guidance.test.ts
+++ b/packages/core/test/reference-guidance.test.ts
@@ -73,4 +73,41 @@ describe("ReferenceGuidance", () => {
       ),
     ),
   )
+
+  it.effect("announces added and removed references as deltas", () => {
+    const reference = (name: string, description: string) =>
+      new Reference.Info({
+        name,
+        path: AbsolutePath.make(`/${name}`),
+        description,
+        source: Reference.LocalSource.make({ type: "local", path: AbsolutePath.make(`/${name}`), description }),
+      })
+    let references = [reference("docs", "Use for product documentation")]
+    return Effect.gen(function* () {
+      const guidance = yield* ReferenceGuidance.Service
+      const initialized = yield* SystemContext.initialize(yield* guidance.load())
+
+      references = [reference("docs", "Use for product documentation"), reference("examples", "Use for examples")]
+      const added = yield* SystemContext.reconcile(yield* guidance.load(), initialized.applied)
+      expect(added).toMatchObject({
+        _tag: "Updated",
+        text: [
+          "New project references are available in addition to those previously listed:",
+          "  <reference>",
+          "    <name>examples</name>",
+          "    <path>/examples</path>",
+          "    <description>Use for examples</description>",
+          "  </reference>",
+        ].join("\n"),
+      })
+
+      references = [reference("examples", "Use for examples")]
+      expect(
+        yield* SystemContext.reconcile(yield* guidance.load(), added._tag === "Updated" ? added.applied : {}),
+      ).toMatchObject({
+        _tag: "Updated",
+        text: "The following project references are no longer available and must not be used: docs.",
+      })
+    }).pipe(Effect.provide(guidanceLayer(Layer.mock(Reference.Service, { list: () => Effect.succeed(references) }))))
+  })
 })
diff --git a/packages/core/test/skill/guidance.test.ts b/packages/core/test/skill/guidance.test.ts
index e7ef9c83ca..b26b75fe71 100644
--- a/packages/core/test/skill/guidance.test.ts
+++ b/packages/core/test/skill/guidance.test.ts
@@ -74,7 +74,73 @@ describe("SkillGuidance", () => {
           .pipe(Effect.flatMap((context) => SystemContext.reconcile(context, initialized.applied))),
       ).toMatchObject({
         _tag: "Updated",
-        text: expect.stringContaining("No skills are currently available."),
+        text: "The following skills are no longer available and must not be used: effect.",
+      })
+    }).pipe(Effect.provide(layer(() => skills)))
+  })
+
+  it.effect("announces added and removed skills as deltas without restating the list", () => {
+    const agent = AgentV2.Info.make(AgentV2.Info.empty(build))
+    const debugging = SkillV2.Info.make({
+      name: "debugging",
+      description: "Diagnose hard bugs",
+      location: AbsolutePath.make(path.resolve("/skills/debugging/SKILL.md")),
+      content: "Debugging guidance",
+    })
+    let skills = [effect]
+    return Effect.gen(function* () {
+      const guidance = yield* SkillGuidance.Service
+      const initialized = yield* guidance
+        .load({ id: agent.id, info: agent })
+        .pipe(Effect.flatMap(SystemContext.initialize))
+
+      skills = [effect, debugging]
+      const added = yield* guidance
+        .load({ id: agent.id, info: agent })
+        .pipe(Effect.flatMap((context) => SystemContext.reconcile(context, initialized.applied)))
+      expect(added).toMatchObject({
+        _tag: "Updated",
+        text: [
+          "New skills are available in addition to those previously listed:",
+          "  <skill>",
+          "    <name>debugging</name>",
+          "    <description>Diagnose hard bugs</description>",
+          "  </skill>",
+        ].join("\n"),
+      })
+
+      skills = [debugging]
+      const removed = yield* guidance
+        .load({ id: agent.id, info: agent })
+        .pipe(
+          Effect.flatMap((context) => SystemContext.reconcile(context, added._tag === "Updated" ? added.applied : {})),
+        )
+      expect(removed).toMatchObject({
+        _tag: "Updated",
+        text: "The following skills are no longer available and must not be used: effect.",
+      })
+    }).pipe(Effect.provide(layer(() => skills)))
+  })
+
+  it.effect("restates the full skill list when a description changes", () => {
+    const agent = AgentV2.Info.make(AgentV2.Info.empty(build))
+    let skills = [effect]
+    return Effect.gen(function* () {
+      const guidance = yield* SkillGuidance.Service
+      const initialized = yield* guidance
+        .load({ id: agent.id, info: agent })
+        .pipe(Effect.flatMap(SystemContext.initialize))
+
+      skills = [SkillV2.Info.make({ ...effect, description: "Build applications with Effect v4" })]
+      expect(
+        yield* guidance
+          .load({ id: agent.id, info: agent })
+          .pipe(Effect.flatMap((context) => SystemContext.reconcile(context, initialized.applied))),
+      ).toMatchObject({
+        _tag: "Updated",
+        text: expect.stringContaining(
+          "The available skills have changed. This list supersedes the previous available skills list.",
+        ),
       })
     }).pipe(Effect.provide(layer(() => skills)))
   })