agentopology 0.3.0 → 0.4.1

package/dist/resolve/phase.js

@@ -0,0 +1,60 @@
+/**
+ * The single answer to "where does an agent with no declared `phase` go?"
+ *
+ * THE BUG THIS FIXES
+ * ------------------
+ * Six consumers each picked their own sentinel, so the same topology ordered
+ * an unphased agent differently on every target:
+ *
+ *   claude-code, claude-workflow  →  Number.MAX_SAFE_INTEGER  →  runs LAST
+ *   gemini-cli                    →  999                      →  runs near-last
+ *   openclaw, kiro, mermaid       →  0                        →  runs FIRST
+ *
+ * An agent that runs first on three targets and last on three others is
+ * precisely the failure "write once, deploy to any platform" exists to prevent.
+ * Found by an audit topology run through `agentopology plan`.
+ *
+ * WHY TRAILING, NOT LEADING
+ * -------------------------
+ * `spec/grammar.md` §7 gives `agent.phase` the default "-- (none, unordered)",
+ * so there is no declared answer — a sort simply needs one. Trailing is the
+ * safer reading: an author who phases *some* agents is expressing "these come
+ * first, in this order", and the ones they did not mention should not leap
+ * ahead of them. A stable sort then preserves declaration order among the
+ * unphased, which is the only ordering information they carry.
+ *
+ * When NO agent declares a phase, every agent takes the same sentinel and the
+ * stable sort leaves declaration order intact — the same result all six
+ * sentinels used to give, which is why this went unnoticed.
+ *
+ * @module
+ */
+/**
+ * Sort key for an agent with no declared `phase`.
+ *
+ * Deliberately `Number.MAX_SAFE_INTEGER` rather than a smaller magic number:
+ * `999` collides with a legitimately declared `phase: 999`, and `0` collides
+ * with `phase: 0`. This one cannot be reached by a real declaration, since
+ * `phase` is parsed with `parseFloat` from a source literal.
+ */
+export const UNPHASED = Number.MAX_SAFE_INTEGER;
+/**
+ * The ordering value for an agent — its declared `phase`, or {@link UNPHASED}.
+ *
+ * Every consumer that sorts by phase must use this. Sorting by
+ * `agent.phase ?? <anything else>` reintroduces the divergence.
+ *
+ * @param agent - Any agent node.
+ * @returns The numeric sort key.
+ */
+export function phaseOf(agent) {
+    return agent.phase ?? UNPHASED;
+}
+/**
+ * Comparator for `Array.prototype.sort`, stable on ties so declaration order
+ * survives among agents sharing a phase.
+ */
+export function byPhase(a, b) {
+    return phaseOf(a) - phaseOf(b);
+}
+//# sourceMappingURL=phase.js.map

package/dist/resolve/phase.js.map

@@ -0,0 +1 @@
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package/dist/scaffold/__tests__/scaffold.test.js

@@ -196,7 +196,10 @@ describe("computeIncrementalPlan", () => {
         fs.writeFileSync(path.join(tmpDir, "gate.sh"), originalScript, "utf-8");
         const manifest = {
             source: "t.at", sourceHash: "x", target: "claude-code",
-            generatedAt: "", files: { "gate.sh": { hash: hashContent(originalScript), category: "script" } },
+            generatedAt: "", files: { "gate.sh": {
+                    hash: hashContent(originalScript),
+                    category: "script"
+                } },
         };
         const files = [
             { path: "gate.sh", content: "#!/bin/bash\necho v2\n", category: "script" },
@@ -211,7 +214,10 @@ describe("computeIncrementalPlan", () => {
         fs.writeFileSync(path.join(tmpDir, "gate.sh"), editedScript, "utf-8");
         const manifest = {
             source: "t.at", sourceHash: "x", target: "claude-code",
-            generatedAt: "", files: { "gate.sh": { hash: hashContent(originalScript), category: "script" } },
+            generatedAt: "", files: { "gate.sh": {
+                    hash: hashContent(originalScript),
+                    category: "script"
+                } },
         };
         const files = [
             { path: "gate.sh", content: "#!/bin/bash\necho v2\n", category: "script" },

package/dist/scaffold/__tests__/scaffold.test.js.map

@@ -1 +1 @@
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package/dist/scaffold/__tests__/settings-merge.test.js

@@ -16,6 +16,11 @@ import * as fs from "node:fs";
 import * as path from "node:path";
 import * as os from "node:os";
 import { deepMergeSettingsJson } from "../merge.js";
+import { mkdtempSync, mkdirSync, writeFileSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+import { computeIncrementalPlan } from "../incremental.js";
+import { hashContent } from "../manifest.js";
 let tmpDir;
 beforeEach(() => {
     tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "settings-merge-test-"));
@@ -124,4 +129,94 @@ describe("Change 3 — deepMergeSettingsJson", () => {
         expect(JSON.parse(result)).toEqual(JSON.parse(generated));
     });
 });
+// ---------------------------------------------------------------------------
+// Regression: the domain-aware merge must actually be REACHED by the scaffold
+// pipeline. It was written and fully tested here, but `incremental.ts` routed
+// `shared-config` to the generic `deepMergeJson`, which keeps the existing
+// value whenever a key exists on both sides and either side is not a plain
+// object. `hooks[event]` is an ARRAY, so:
+//   - adding a hook to an event the file already declared silently DROPPED it
+//   - removing a hook was impossible, since the generic merge never deletes
+// ---------------------------------------------------------------------------
+describe("settings.json merge is wired into the scaffold pipeline", () => {
+    const settings = (obj) => JSON.stringify(obj, null, 2);
+    const plan = (existing, generated) => {
+        const dir = mkdtempSync(join(tmpdir(), "at-settings-"));
+        const rel = ".claude/settings.json";
+        mkdirSync(join(dir, ".claude"), { recursive: true });
+        writeFileSync(join(dir, rel), existing);
+        const generatedFiles = [
+            { path: rel, content: generated, category: "shared-config" },
+        ];
+        const manifest = {
+            source: "t.at",
+            sourceHash: "x",
+            target: "claude-code",
+            generatedAt: new Date().toISOString(),
+            files: { [rel]: { hash: hashContent(existing), category: "shared-config" } },
+        };
+        const actions = computeIncrementalPlan(dir, "claude-code", generatedFiles, manifest);
+        rmSync(dir, { recursive: true, force: true });
+        const action = actions.find((a) => a.path === rel);
+        // FileAction is a union; only the writing variants carry content.
+        return action;
+    };
+    it("adds a hook to an event the existing file already declares", () => {
+        const existing = settings({
+            hooks: { SubagentStop: [{ matcher: "old", hooks: [{ type: "command", command: "a.sh" }] }] },
+        });
+        const generated = settings({
+            hooks: {
+                SubagentStop: [
+                    { matcher: "old", hooks: [{ type: "command", command: "a.sh" }] },
+                    { matcher: "new", hooks: [{ type: "command", command: "b.sh" }] },
+                ],
+            },
+        });
+        const action = plan(existing, generated);
+        expect(action.type).toBe("update");
+        // The generic merge kept the one-entry array and this assertion failed.
+        expect(action.content).toContain("b.sh");
+    });
+    it("removes a hook when the topology no longer declares one", () => {
+        const existing = settings({
+            permissions: { allow: ["Read"] },
+            hooks: { SubagentStop: [{ matcher: "gone", hooks: [{ type: "command", command: "x.sh" }] }] },
+        });
+        const generated = settings({ permissions: { allow: ["Read"] } });
+        const action = plan(existing, generated);
+        expect(action.type).toBe("update");
+        expect(action.content).not.toContain("x.sh");
+        // The user's own permissions must survive the removal.
+        expect(action.content).toContain("Read");
+    });
+    it("still unions permissions the user added by hand", () => {
+        const existing = settings({ permissions: { allow: ["Read", "MyOwnTool"] } });
+        const generated = settings({ permissions: { allow: ["Read", "Write"] } });
+        const action = plan(existing, generated);
+        expect(action.content).toContain("MyOwnTool");
+        expect(action.content).toContain("Write");
+    });
+    it("leaves non-settings shared-config on the generic merge", () => {
+        const dir = mkdtempSync(join(tmpdir(), "at-cfg-"));
+        const rel = ".claude/other.json";
+        mkdirSync(join(dir, ".claude"), { recursive: true });
+        const existing = JSON.stringify({ hooks: { A: [1] }, keep: true }, null, 2);
+        writeFileSync(join(dir, rel), existing);
+        const manifest = {
+            source: "t.at",
+            sourceHash: "x",
+            target: "claude-code",
+            generatedAt: new Date().toISOString(),
+            files: { [rel]: { hash: hashContent(existing), category: "shared-config" } },
+        };
+        const actions = computeIncrementalPlan(dir, "claude-code", [{ path: rel, content: JSON.stringify({ added: 1 }, null, 2), category: "shared-config" }], manifest);
+        rmSync(dir, { recursive: true, force: true });
+        const action = actions.find((a) => a.path === rel);
+        const written = action;
+        // Generic merge never deletes, so the existing hooks key survives here.
+        expect(written.content).toContain("hooks");
+        expect(written.content).toContain("added");
+    });
+});
 //# sourceMappingURL=settings-merge.test.js.map

package/dist/scaffold/__tests__/settings-merge.test.js.map

@@ -1 +1 @@
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package/dist/scaffold/incremental.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"incremental.d.ts","sourceRoot":"","sources":["../../src/scaffold/incremental.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAG/D;;;;;;;;;;;GAWG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,cAAc,EAAE,aAAa,EAAE,EAC/B,QAAQ,EAAE,gBAAgB,GAAG,IAAI,GAChC,UAAU,EAAE,CAgHd;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,UAAU,EAAE,EACrB,OAAO,EAAE;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,OAAO,CAAA;CAAE,GAC1C;IACD,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB,CAyDA"}
+{"version":3,"file":"incremental.d.ts","sourceRoot":"","sources":["../../src/scaffold/incremental.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAQ/D;;;;;;;;;;;GAWG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,cAAc,EAAE,aAAa,EAAE,EAC/B,QAAQ,EAAE,gBAAgB,GAAG,IAAI,GAChC,UAAU,EAAE,CA2Hd;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,UAAU,EAAE,EACrB,OAAO,EAAE;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,OAAO,CAAA;CAAE,GAC1C;IACD,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB,CAyDA"}

package/dist/scaffold/incremental.js

@@ -9,7 +9,7 @@
  */
 import { chmodSync, existsSync, mkdirSync, readFileSync, unlinkSync, writeFileSync } from "node:fs";
 import { dirname, join } from "node:path";
-import { mergeAgentFile, shouldOverwriteScript, deepMergeJson } from "./merge.js";
+import { mergeAgentFile, shouldOverwriteScript, deepMergeJson, deepMergeSettingsJson, } from "./merge.js";
 /**
  * Compute an incremental scaffold plan.
  *
@@ -89,7 +89,18 @@ export function computeIncrementalPlan(basePath, target, generatedFiles, manifes
                 break;
             }
             case "shared-config": {
-                const merged = deepMergeJson(existingContent, file.content);
+                // settings.json needs the DOMAIN-AWARE merge, not the generic one.
+                // The generic `deepMergeJson` keeps the existing value whenever a key
+                // exists on both sides and either side is not a plain object — and
+                // `hooks[event]` is an ARRAY. So adding a hook to an event the file
+                // already declares silently dropped it, and removing a hook was
+                // impossible. `deepMergeSettingsJson` unions permissions, merges env,
+                // and lets the topology own `hooks` outright (including deleting it).
+                // It was written and fully tested but never reachable until now.
+                const isSettings = /(^|\/)settings\.json$/.test(file.path);
+                const merged = isSettings
+                    ? deepMergeSettingsJson(existingContent, file.content)
+                    : deepMergeJson(existingContent, file.content);
                 if (merged === existingContent) {
                     actions.push({ type: "unchanged", path: file.path });
                 }

package/dist/scaffold/incremental.js.map

@@ -1 +1 @@
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package/dist/visualizer/__tests__/topology-brain-link.test.js

@@ -3,10 +3,25 @@ import { parse } from "../../parser/index.js";
 import { generateVisualization } from "../index.js";
 /** A minimal topology with one brain store. */
 const ONE_BRAIN = `topology cb : [brain] {
-  meta { version: "1.0.0" description: "x" }
-  memory { store brain { type: brain path: "brain/" format: obsidian } }
-  agent lib { model: sonnet description: "k" tools: [Read, Write] custodian-of: [brain] }
-  action intake { kind: inline description: "in" }
+  meta {
+    version: "1.0.0"
+    description: "x"
+  }
+  memory { store brain {
+    type: brain
+    path: "brain/"
+    format: obsidian
+  } }
+  agent lib {
+    model: sonnet
+    description: "k"
+    tools: [Read, Write]
+    custodian-of: [brain]
+  }
+  action intake {
+    kind: inline
+    description: "in"
+  }
   flow { intake -> lib }
 }`;
 describe("Topology visualizer — brain cross-link", () => {

package/dist/visualizer/__tests__/topology-brain-link.test.js.map

@@ -1 +1 @@
-{"version":3,"file":"topology-brain-link.test.js","sourceRoot":"","sources":["../../../src/visualizer/__tests__/topology-brain-link.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAC;AAC9C,OAAO,EAAE,qBAAqB,EAAE,MAAM,aAAa,CAAC;AAEpD,+CAA+C;AAC/C,MAAM,SAAS,GAAG;;;;;;EAMhB,CAAC;AAEH,QAAQ,CAAC,wCAAwC,EAAE,GAAG,EAAE;IACtD,4EAA4E;IAC5E,4EAA4E;IAC5E,EAAE,CAAC,mDAAmD,EAAE,GAAG,EAAE;QAC3D,MAAM,IAAI,GAAG,qBAAqB,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC;QACrD,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;QACzC,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;IAC3C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,sDAAsD,EAAE,GAAG,EAAE;QAC9D,MAAM,IAAI,GAAG,qBAAqB,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE;YACnD,MAAM,EAAE,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,qBAAqB,EAAE,CAAC;SACvD,CAAC,CAAC;QACH,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;QACrC,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,4BAA4B,CAAC,CAAC;QACrD,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,gCAAgC;IAC5E,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,8DAA8D,EAAE,GAAG,EAAE;QACtE,MAAM,IAAI,GAAG,qBAAqB,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE;YACnD,MAAM,EAAE;gBACN,EAAE,EAAE,EAAE,cAAc,EAAE,IAAI,EAAE,4BAA4B,EAAE;gBAC1D,EAAE,EAAE,EAAE,gBAAgB,EAAE,IAAI,EAAE,8BAA8B,EAAE;aAC/D;SACF,CAAC,CAAC;QACH,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;QACrC,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,mCAAmC,CAAC,CAAC;QAC5D,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,qCAAqC,CAAC,CAAC;QAC9D,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,8BAA8B;IAC1E,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
+{"version":3,"file":"topology-brain-link.test.js","sourceRoot":"","sources":["../../../src/visualizer/__tests__/topology-brain-link.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAC;AAC9C,OAAO,EAAE,qBAAqB,EAAE,MAAM,aAAa,CAAC;AAEpD,+CAA+C;AAC/C,MAAM,SAAS,GAAG;;;;;;;;;;;;;;;;;;;;;EAqBhB,CAAC;AAEH,QAAQ,CAAC,wCAAwC,EAAE,GAAG,EAAE;IACtD,4EAA4E;IAC5E,4EAA4E;IAC5E,EAAE,CAAC,mDAAmD,EAAE,GAAG,EAAE;QAC3D,MAAM,IAAI,GAAG,qBAAqB,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC;QACrD,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;QACzC,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;IAC3C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,sDAAsD,EAAE,GAAG,EAAE;QAC9D,MAAM,IAAI,GAAG,qBAAqB,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE;YACnD,MAAM,EAAE,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,qBAAqB,EAAE,CAAC;SACvD,CAAC,CAAC;QACH,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;QACrC,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,4BAA4B,CAAC,CAAC;QACrD,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,gCAAgC;IAC5E,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,8DAA8D,EAAE,GAAG,EAAE;QACtE,MAAM,IAAI,GAAG,qBAAqB,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE;YACnD,MAAM,EAAE;gBACN,EAAE,EAAE,EAAE,cAAc,EAAE,IAAI,EAAE,4BAA4B,EAAE;gBAC1D,EAAE,EAAE,EAAE,gBAAgB,EAAE,IAAI,EAAE,8BAA8B,EAAE;aAC/D;SACF,CAAC,CAAC;QACH,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;QACrC,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,mCAAmC,CAAC,CAAC;QAC5D,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,qCAAqC,CAAC,CAAC;QAC9D,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,8BAA8B;IAC1E,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/examples/code-review.at

@@ -50,7 +50,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: analyzer
     model: sonnet
     permissions: supervised
-    prompt: "prompts/analyzer.md"
+    prompt {
+      Read the diff at workspace/pr-diff.md.
+
+      Report structural risk only — complexity, dependency changes, and blast
+      radius. Do not comment on security; a separate agent covers that.
+
+      Write your findings to workspace/analysis.md and set risk-level.
+    }
     phase: 1
     tools: [Read, Grep, Glob]
     reads: ["workspace/pr-diff.md"]
@@ -64,7 +71,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: security
     model: sonnet
     permissions: supervised
-    prompt: "prompts/security-scanner.md"
+    prompt {
+      Read the diff at workspace/pr-diff.md.
+
+      Look for injection, auth or authorization changes, secret handling, and
+      unsafe deserialization. Do not comment on style or complexity.
+
+      Write your findings to workspace/security.md and set has-vulnerabilities.
+    }
     phase: 1
     tools: [Read, Grep, Glob]
     reads: ["workspace/pr-diff.md"]
@@ -79,7 +93,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: reviewer
     model: opus
     permissions: supervised
-    prompt: "prompts/reviewer.md"
+    prompt {
+      Read the diff, workspace/analysis.md and workspace/security.md.
+
+      The two reports were produced independently. Where they disagree, say so
+      rather than silently picking one.
+
+      Write your review to workspace/review.md and set a verdict.
+    }
     phase: 2
     tools: [Read, Grep, Glob]
     reads: ["workspace/pr-diff.md", "workspace/analysis.md", "workspace/security.md"]
@@ -93,7 +114,14 @@ topology code-review : [pipeline, fan-out, human-gate] {
     role: reporter
     model: haiku
     permissions: autonomous
-    prompt: "prompts/reporter.md"
+    prompt {
+      Read workspace/analysis.md, workspace/security.md and workspace/review.md.
+
+      Produce one report a human can act on: the verdict, the reasons behind it,
+      and the specific changes required. No new analysis.
+
+      Write it to workspace/final-report.md.
+    }
     phase: 3
     tools: [Read, Write, Glob]
     reads: ["workspace/analysis.md", "workspace/security.md", "workspace/review.md"]

package/examples/data-processing.at

@@ -103,7 +103,15 @@ topology data-processing : [pipeline, fan-out] {
     role: extractor
     model: sonnet
     permissions: autonomous
-    prompt: "prompts/extractor.md"
+    prompt {
+      Read source documents from workspace/raw/.
+
+      Extract their text and structure using the extract-pdf and extract-doc
+      tools. Preserve tables and headings — downstream classification depends
+      on them.
+
+      Write one extracted file per source into workspace/extracted/.
+    }
     phase: 1
     tools: [Read, Write, extract-pdf, extract-doc]
     skills: [extraction]
@@ -123,7 +131,14 @@ topology data-processing : [pipeline, fan-out] {
     role: classifier
     model: haiku
     permissions: autonomous
-    prompt: "prompts/classifier.md"
+    prompt {
+      Read extracted documents from workspace/extracted/.
+
+      Assign each one a category and confidence. Run validate-output on your
+      result before writing it.
+
+      Write classified records into workspace/classified/.
+    }
     phase: 2
     tools: [Read, Write, validate-output]
     skills: [classification]
@@ -143,7 +158,14 @@ topology data-processing : [pipeline, fan-out] {
     role: synthesizer
     model: opus
     permissions: autonomous
-    prompt: "prompts/synthesizer.md"
+    prompt {
+      Read all classified records from workspace/classified/.
+
+      Merge them with merge-results into a single structured view. Where records
+      conflict, keep both and mark the conflict rather than choosing.
+
+      Write the result to workspace/synthesis.json.
+    }
     phase: 3
     tools: [Read, Write, merge-results]
     reads: ["workspace/classified/"]
@@ -154,7 +176,14 @@ topology data-processing : [pipeline, fan-out] {
     role: reporter
     model: sonnet
     permissions: autonomous
-    prompt: "prompts/reporter.md"
+    prompt {
+      Read workspace/synthesis.json.
+
+      Produce a report for a human reader: what was processed, what was found,
+      and what remains unresolved. No new analysis.
+
+      Write workspace/report.md and workspace/report.pdf, then set quality.
+    }
     phase: 4
     tools: [Read, Write]
     reads: ["workspace/synthesis.json"]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentopology",
-  "version": "0.3.0",
+  "version": "0.4.1",
   "description": "The declarative language for multi-agent systems. Write once, scaffold for any platform.",
   "author": "Nadav Naveh",
   "license": "Apache-2.0",

package/spec/grammar.md

@@ -43,6 +43,30 @@ template-var     = [A-Z] [A-Z0-9_-]*
 
 **Rule:** Quote strings. Don't quote identifiers, numbers, or booleans.
 
+**Rule: one field per line.** Key-value fields are newline-separated. Writing two
+on one line makes the first key take the rest of the line as its value:
+
+```
+# WRONG — `model` becomes the string "sonnet retry: 3"
+agent a { model: sonnet retry: 3 }
+
+# RIGHT
+agent a {
+  model: sonnet
+  retry: 3
+}
+```
+
+This is not a parser limitation to route around — some unquoted values are
+legitimately multi-token (`on-fail: fallback reviewer`), so whitespace could not
+separate fields without ambiguity. V90 rejects the collapsed form, in `meta` and in every node block.
+
+**Exception:** free-prose fields (`description`, `role`, `generates`,
+`termination`) are exempt once their quotes have been stripped by the parser,
+because a colon in English is ordinary — `description: "Demo: agent pipeline"`.
+Where quotes survive parsing the check is still sharp: one well-formed quoted
+token followed by more content means a field was eaten.
+
 ### Composite Types
 
 ```ebnf
@@ -347,7 +371,7 @@ scale-field     = 'mode' ':' ('auto' | 'fixed' | 'config')
 | `role` | identifier | no | -- | Maps to a role defined in the `roles` block |
 | `model` | model-id | yes | -- | LLM model identifier (e.g., `opus`, `gpt-4o`, `gemini-pro`) |
 | `permissions` | perm-enum | no | `autonomous` | Permission mode |
-| `prompt` | block | no | -- | Inline agent instructions (multi-line text block) |
+| `prompt` | block | no | -- | Inline agent instructions (multi-line text **block**). A key-value `prompt: "path"` is NOT valid on an agent — that form belongs to `skill` — and is rejected by V89. |
 | `phase` | number | no | -- | Pipeline position (ordering by numeric value) |
 | `tools` | tool-list | no | all | Tool allowlist |
 | `disallowed-tools` | tool-list | no | `[]` | Explicit deny-list |