agentopology 0.5.2 → 0.7.0

package/dist/scaffold/merge.js

@@ -9,6 +9,7 @@
  */
 import { extractSectionUntilKnownHeading, CLAUDE_CODE_STRUCTURAL_HEADINGS, COPILOT_STRUCTURAL_HEADINGS, } from "../sync/index.js";
 import { hashContent } from "./manifest.js";
+import { fenceSpan } from "../bindings/lib/prompt-fence.js";
 /**
  * Return the list of known structural headings for a binding.
  * Falls back to the Claude Code list for unknown bindings.
@@ -38,6 +39,19 @@ function getStructuralHeadings(binding) {
  * @returns Merged file content
  */
 export function mergeAgentFile(existing, generated, binding) {
+    // Files with prompt markers: keep the user's text between them, take
+    // everything else from the generated file.
+    const mine = fenceSpan(existing);
+    const theirs = fenceSpan(generated);
+    if (mine && theirs) {
+        return generated.slice(0, theirs.start) + existing.slice(mine.start, mine.end) + generated.slice(theirs.end);
+    }
+    // A file from before the markers: its instructions move inside them once.
+    if (theirs) {
+        const legacy = extractSectionUntilKnownHeading(existing, "## Instructions", getStructuralHeadings(binding));
+        if (legacy !== null)
+            return generated.slice(0, theirs.start) + "\n" + legacy + "\n" + generated.slice(theirs.end);
+    }
     const structuralHeadings = getStructuralHeadings(binding);
     // Extract the HUMAN zone from the existing file
     const humanContent = extractSectionUntilKnownHeading(existing, "## Instructions", structuralHeadings);
@@ -107,24 +121,38 @@ export function deepMergeJson(existingRaw, generatedRaw) {
         return existingRaw;
     }
     const merged = mergeObjects(existing, generated);
+    // Nothing to add: keep the user's bytes, formatting included.
+    if (JSON.stringify(merged) === JSON.stringify(existing))
+        return existingRaw;
     return JSON.stringify(merged, null, 2) + "\n";
 }
 /**
  * Merge settings.json files with domain-aware logic for Claude Code settings.
  *
+ * The user's file is the base; scaffold only adds or replaces what it owns.
+ *
  * Rules:
- *   - permissions.allow: union-merge (deduplicated)
- *   - permissions.deny: union-merge (deduplicated)
+ *   - permissions: every existing key is kept (ask, defaultMode,
+ *     additionalDirectories, ...); allow, deny and ask arrays are
+ *     union-merged; a generated scalar is added only where none exists
  *   - env: shallow-merge (generated wins on key conflict)
- *   - hooks: rewritten entirely from generated (topology owns hooks)
+ *   - hooks: a hook group is the topology's when one of its commands names a
+ *     path in `ownedPaths`; those are replaced by the generated hooks, and
+ *     every other group — the user's — is kept. Without `ownedPaths`, nothing
+ *     existing is treated as owned, so nothing is removed
  *   - All other top-level keys: existing wins (user-only keys preserved)
  *
+ * This used to rebuild permissions from allow/deny alone and replace hooks
+ * wholesale, so a re-scaffold deleted the user's own hooks, ask rules and
+ * defaultMode, and two topologies in one repo deleted each other's hooks.
+ *
  * @param existingRaw - Current settings.json content on disk (JSON string, or empty string)
  * @param generatedRaw - Freshly generated settings.json content (JSON string)
+ * @param ownedPaths - Paths this topology writes or wrote (generated + manifest)
  * @returns Merged JSON string
  * @throws {Error} if existingRaw is non-empty and is invalid JSON
  */
-export function deepMergeSettingsJson(existingRaw, generatedRaw) {
+export function deepMergeSettingsJson(existingRaw, generatedRaw, ownedPaths = []) {
     // Empty existing means first scaffold — return generated unchanged
     if (existingRaw.trim() === "") {
         return generatedRaw;
@@ -145,22 +173,35 @@ export function deepMergeSettingsJson(existingRaw, generatedRaw) {
     }
     // Start with existing (preserves all user-only top-level keys)
     const merged = { ...existing };
-    // --- permissions: union-merge allow and deny arrays ---
-    const existingPerms = (existing.permissions ?? {});
-    const generatedPerms = (generated.permissions ?? {});
-    if (generated.permissions !== undefined || existing.permissions !== undefined) {
-        const mergedPerms = {};
-        for (const key of ["allow", "deny"]) {
-            const ex = Array.isArray(existingPerms[key]) ? existingPerms[key] : [];
-            const gen = Array.isArray(generatedPerms[key]) ? generatedPerms[key] : [];
-            const union = Array.from(new Set([...ex, ...gen]));
-            if (union.length > 0) {
+    // --- permissions: keep every existing key; union the rule arrays ---
+    if (isPlainObject(generated.permissions) || isPlainObject(existing.permissions)) {
+        const ex = isPlainObject(existing.permissions) ? existing.permissions : {};
+        const gen = isPlainObject(generated.permissions) ? generated.permissions : {};
+        const mergedPerms = { ...ex };
+        for (const [key, value] of Object.entries(gen)) {
+            const current = mergedPerms[key];
+            if (Array.isArray(value) || Array.isArray(current)) {
+                const union = Array.from(new Set([
+                    ...(Array.isArray(current) ? current : []),
+                    ...(Array.isArray(value) ? value : []),
+                ]));
                 mergedPerms[key] = union;
             }
+            else if (current === undefined) {
+                mergedPerms[key] = value;
+            }
+        }
+        for (const key of Object.keys(mergedPerms)) {
+            if (Array.isArray(mergedPerms[key]) && mergedPerms[key].length === 0) {
+                delete mergedPerms[key];
+            }
         }
         if (Object.keys(mergedPerms).length > 0) {
             merged.permissions = mergedPerms;
         }
+        else {
+            delete merged.permissions;
+        }
     }
     // --- env: shallow-merge, generated wins on conflict ---
     if (generated.env !== undefined) {
@@ -168,12 +209,12 @@ export function deepMergeSettingsJson(existingRaw, generatedRaw) {
         const generatedEnv = generated.env;
         merged.env = { ...existingEnv, ...generatedEnv };
     }
-    // --- hooks: rewritten entirely from generated (topology owns hooks) ---
-    if (generated.hooks !== undefined) {
-        merged.hooks = generated.hooks;
+    // --- hooks: replace the topology's own groups, keep the user's ---
+    const mergedHooks = mergeHooks(existing.hooks, generated.hooks, ownedPaths);
+    if (mergedHooks) {
+        merged.hooks = mergedHooks;
     }
     else {
-        // No hooks in generated — remove the hooks key (topology no longer declares any)
         delete merged.hooks;
     }
     // --- all other generated keys: add if missing, do NOT overwrite existing ---
@@ -184,8 +225,72 @@ export function deepMergeSettingsJson(existingRaw, generatedRaw) {
             merged[key] = value;
         }
     }
+    // Nothing to add: keep the user's bytes, formatting included.
+    if (JSON.stringify(merged) === JSON.stringify(existing))
+        return existingRaw;
     return JSON.stringify(merged, null, 2) + "\n";
 }
+function isPlainObject(v) {
+    return v !== null && typeof v === "object" && !Array.isArray(v);
+}
+/**
+ * Identity of a hook group for deduplication: matcher plus each command with
+ * the project-dir prefix, quotes and "./" removed. An imported hook written
+ * as `bash .claude/hooks/x.sh` and the same hook compiled as
+ * `bash "$CLAUDE_PROJECT_DIR/.claude/hooks/x.sh"` are one hook, not two that
+ * both fire.
+ */
+function hookGroupKey(group) {
+    if (!isPlainObject(group) || !Array.isArray(group.hooks))
+        return JSON.stringify(group);
+    const commands = group.hooks.map((h) => isPlainObject(h) && typeof h.command === "string"
+        ? h.command.replace(/"?\$CLAUDE_PROJECT_DIR\/?/g, "").replace(/["']/g, "").replace(/(^|\s)\.\//g, "$1").replace(/\s+/g, " ").trim()
+        : JSON.stringify(h));
+    return JSON.stringify([group.matcher ?? "", commands]);
+}
+/** Whether a hook group runs a script this topology owns. */
+function isOwnedHookGroup(group, scripts) {
+    if (!isPlainObject(group) || !Array.isArray(group.hooks))
+        return false;
+    return group.hooks.some((h) => {
+        if (!isPlainObject(h) || typeof h.command !== "string")
+            return false;
+        const tokens = h.command.split(/\s+/).map((t) => t.replace(/^\.\//, ""));
+        return tokens.some((t) => scripts.includes(t));
+    });
+}
+/**
+ * Per event: the user's groups first, then the generated ones, deduplicated.
+ * Returns undefined when no event keeps any group.
+ */
+function mergeHooks(existingHooks, generatedHooks, ownedPaths) {
+    // Config files are never hook scripts; matching them would claim a user hook
+    // that merely mentions CLAUDE.md.
+    const scripts = ownedPaths
+        .filter((p) => !/\.(md|json)$/.test(p))
+        .map((p) => p.replace(/^\.\//, ""));
+    const ex = isPlainObject(existingHooks) ? existingHooks : {};
+    const gen = isPlainObject(generatedHooks) ? generatedHooks : {};
+    const out = {};
+    for (const event of new Set([...Object.keys(ex), ...Object.keys(gen)])) {
+        // A group generated again stays where it is, so reruns (and two
+        // topologies taking turns) do not reorder the file.
+        const regenerated = new Set((Array.isArray(gen[event]) ? gen[event] : []).map(hookGroupKey));
+        const kept = (Array.isArray(ex[event]) ? ex[event] : []).filter((g) => regenerated.has(hookGroupKey(g)) || !isOwnedHookGroup(g, scripts));
+        const seen = new Set();
+        const groups = [];
+        for (const g of [...kept, ...(Array.isArray(gen[event]) ? gen[event] : [])]) {
+            const key = hookGroupKey(g);
+            if (seen.has(key))
+                continue;
+            seen.add(key);
+            groups.push(g);
+        }
+        if (groups.length > 0)
+            out[event] = groups;
+    }
+    return Object.keys(out).length > 0 ? out : undefined;
+}
 function mergeObjects(existing, generated) {
     // Start with a copy of existing (preserves user-only keys)
     const result = { ...existing };

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package/dist/scaffold/types.d.ts

@@ -49,5 +49,22 @@ export type FileAction = {
     path: string;
     content: string;
     detail: string;
+}
+/**
+ * Never written or deleted, even with --force. `unsafe` marks a path that
+ * must abort the whole run before anything is written (an empty or
+ * malformed file name — the EISDIR class).
+ */
+ | {
+    type: "blocked";
+    path: string;
+    detail: string;
+    unsafe?: boolean;
+}
+/** A create-only file already there: the user's. Never written or claimed. */
+ | {
+    type: "kept";
+    path: string;
+    detail: string;
 };
 //# sourceMappingURL=types.d.ts.map

package/dist/scaffold/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/scaffold/types.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,+CAA+C;AAC/C,MAAM,WAAW,aAAa;IAC5B,2DAA2D;IAC3D,IAAI,EAAE,MAAM,CAAC;IACb,6EAA6E;IAC7E,QAAQ,EAAE,SAAS,GAAG,OAAO,GAAG,QAAQ,GAAG,eAAe,CAAC;CAC5D;AAED,wDAAwD;AACxD,MAAM,WAAW,gBAAgB;IAC/B,4BAA4B;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,8DAA8D;IAC9D,UAAU,EAAE,MAAM,CAAC;IACnB,gDAAgD;IAChD,MAAM,EAAE,MAAM,CAAC;IACf,6DAA6D;IAC7D,WAAW,EAAE,MAAM,CAAC;IACpB,4DAA4D;IAC5D,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC;CACtC;AAED,yEAAyE;AACzE,MAAM,MAAM,UAAU,GAClB;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,OAAO,CAAA;CAAE,GACvE;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,OAAO,CAAA;CAAE,GACvF;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAChC;IAAE,IAAI,EAAE,WAAW,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GACnC;IAAE,IAAI,EAAE,UAAU,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/scaffold/types.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,+CAA+C;AAC/C,MAAM,WAAW,aAAa;IAC5B,2DAA2D;IAC3D,IAAI,EAAE,MAAM,CAAC;IACb,6EAA6E;IAC7E,QAAQ,EAAE,SAAS,GAAG,OAAO,GAAG,QAAQ,GAAG,eAAe,CAAC;CAC5D;AAED,wDAAwD;AACxD,MAAM,WAAW,gBAAgB;IAC/B,4BAA4B;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,8DAA8D;IAC9D,UAAU,EAAE,MAAM,CAAC;IACnB,gDAAgD;IAChD,MAAM,EAAE,MAAM,CAAC;IACf,6DAA6D;IAC7D,WAAW,EAAE,MAAM,CAAC;IACpB,4DAA4D;IAC5D,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC;CACtC;AAED,yEAAyE;AACzE,MAAM,MAAM,UAAU,GAClB;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,OAAO,CAAA;CAAE,GACvE;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,OAAO,CAAA;CAAE,GACvF;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAChC;IAAE,IAAI,EAAE,WAAW,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GACnC;IAAE,IAAI,EAAE,UAAU,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE;AACrE;;;;GAIG;GACD;IAAE,IAAI,EAAE,SAAS,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE;AACrE,8EAA8E;GAC5E;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC"}

package/dist/sync/index.d.ts

@@ -3,6 +3,7 @@
  * and writes it back into .at file prompt {} blocks.
  * @module
  */
+export { PROMPT_FENCE_OPEN, PROMPT_FENCE_CLOSE, fencedPrompt } from "../bindings/lib/prompt-fence.js";
 /** A platform file with its path and content. */
 export interface PlatformFile {
     path: string;

package/dist/sync/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/sync/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,iDAAiD;AACjD,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAQD;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,YAAY,EAAE,EACrB,OAAO,EAAE,MAAM,GACd,MAAM,CAqBR;AAsCD,4FAA4F;AAC5F,eAAO,MAAM,+BAA+B,UAM3C,CAAC;AAEF,4DAA4D;AAC5D,eAAO,MAAM,2BAA2B,UAMvC,CAAC;AA8LF;;;;;;;;GAQG;AACH,wBAAgB,+BAA+B,CAC7C,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,MAAM,EAAE,GACtB,MAAM,GAAG,IAAI,CAgCf"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/sync/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAMH,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,YAAY,EAAE,MAAM,iCAAiC,CAAC;AAQtG,iDAAiD;AACjD,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAQD;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,YAAY,EAAE,EACrB,OAAO,EAAE,MAAM,GACd,MAAM,CAqBR;AAmED,4FAA4F;AAC5F,eAAO,MAAM,+BAA+B,UAM3C,CAAC;AAEF,4DAA4D;AAC5D,eAAO,MAAM,2BAA2B,UAMvC,CAAC;AA8LF;;;;;;;;GAQG;AACH,wBAAgB,+BAA+B,CAC7C,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,MAAM,EAAE,GACtB,MAAM,GAAG,IAAI,CAgCf"}

package/dist/sync/index.js

@@ -4,6 +4,14 @@
  * @module
  */
 import { escapeRegex } from "../parser/lexer.js";
+import { parse } from "../parser/index.js";
+import { claudeCodeBinding } from "../bindings/claude-code.js";
+export { PROMPT_FENCE_OPEN, PROMPT_FENCE_CLOSE, fencedPrompt } from "../bindings/lib/prompt-fence.js";
+import { fencedPrompt } from "../bindings/lib/prompt-fence.js";
+/** Undo the binding's heading downshift (### → ##), so a prompt round-trips unchanged. */
+function upshiftHeadings(text) {
+    return text.replace(/^#(#{2,6})(\s)/gm, "$1$2");
+}
 /**
  * Sync prompt content from platform agent files back into an .at source string.
  *
@@ -16,7 +24,7 @@ export function syncFromPlatform(atSource, files, binding) {
     let prompts;
     switch (binding) {
         case "claude-code":
-            prompts = extractClaudeCodePrompts(files);
+            prompts = withoutUnchanged(atSource, extractClaudeCodePrompts(files), files);
             break;
         case "codex":
             prompts = extractCodexPrompts(files);
@@ -32,6 +40,32 @@ export function syncFromPlatform(atSource, files, binding) {
     }
     return insertPromptBlocks(atSource, prompts);
 }
+/**
+ * Drop prompts whose fenced text is exactly what scaffold would write from the
+ * .at as it stands: sync brings back edits, never the generator's own output
+ * (a description-only agent would otherwise gain a prompt block on every sync).
+ */
+function withoutUnchanged(atSource, prompts, files) {
+    let generated;
+    const warn = console.warn;
+    console.warn = () => { };
+    try {
+        generated = new Map(claudeCodeBinding.scaffold(parse(atSource))
+            .map((f) => [f.path.match(/agents\/([^/]+)\/AGENT\.md$/)?.[1] ?? "", fencedPrompt(f.content)])
+            .filter(([id]) => id !== ""));
+    }
+    catch {
+        return prompts;
+    }
+    finally {
+        console.warn = warn;
+    }
+    const onDisk = new Map(files.map((f) => [f.path.match(/agents[\\/]([^\\/]+)[\\/]AGENT\.md$/)?.[1] ?? "", fencedPrompt(f.content)]));
+    return prompts.filter((p) => {
+        const disk = onDisk.get(p.agentId);
+        return disk === null || disk === undefined || disk !== generated.get(p.agentId);
+    });
+}
 // ---------------------------------------------------------------------------
 // Per-binding extractors
 // ---------------------------------------------------------------------------
@@ -51,7 +85,11 @@ function extractClaudeCodePrompts(files) {
         if (!match)
             continue;
         const agentId = match[1];
-        const content = extractSectionUntilKnownHeading(file.content, "## Instructions", CLAUDE_CODE_STRUCTURAL_HEADINGS);
+        const fenced = fencedPrompt(file.content);
+        // Files scaffolded before the markers: the old heuristic.
+        const content = fenced !== null
+            ? upshiftHeadings(fenced)
+            : extractSectionUntilKnownHeading(file.content, "## Instructions", CLAUDE_CODE_STRUCTURAL_HEADINGS);
         if (content) {
             prompts.push({ agentId, content });
         }

package/dist/sync/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentopology",
-  "version": "0.5.2",
+  "version": "0.7.0",
   "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

@@ -368,6 +368,7 @@ scale-field     = 'mode' ':' ('auto' | 'fixed' | 'config')
 
 | Field | Type | Required | Default | Description |
 |-------|------|----------|---------|-------------|
+| `file` | string | no | -- | Project-relative path of the hand-written file holding this node's internals. Bindings reference it and never generate or overwrite it (V97). `import` sets it on every file it did not generate, so a hand-built system comes in without losing anything. |
 | `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 |
@@ -1088,7 +1089,7 @@ Environment blocks have no fixed schema -- fields are identifier/string key-valu
 ```ebnf
 triggers        = 'triggers' '{' command-decl* '}'
 command-decl    = 'command' identifier '{' command-fields '}'
-command-fields  = 'pattern' ':' string ('argument' ':' template-var)?
+command-fields  = 'pattern' ':' string ('argument' ':' template-var)? ('file' ':' string)?
 ```
 
 ```agenttopology
@@ -1108,6 +1109,7 @@ triggers {
 |-------|------|----------|---------|
 | `pattern` | string | yes | -- |
 | `argument` | template-var | no | -- |
+| `file` | string | no | -- |
 
 ---
 
@@ -1117,9 +1119,12 @@ triggers {
 hooks           = 'hooks' '{' hook-decl* '}'
 hook-decl       = 'hook' identifier '{' hook-fields '}'
 hook-fields     = ('on' ':' hook-event | 'matcher' ':' string | 'run' ':' string
-                  | 'type' ':' hook-type | 'timeout' ':' number)*
-hook-event      = <universal-event> | <platform-event>
-hook-type       = 'command' | 'prompt'
+                  | 'type' ':' hook-type | 'flag' ':' env-name | 'timeout' ':' number)*
+hook-event      = <universal-event> | <platform-event> | <engine-event>
+hook-type       = 'command' | 'prompt' | 'mod'
+engine-event    = 'tool.call' | 'prompt.submit' | 'prompt.context' | 'session.start'
+                | 'session.end' | 'model.complete' | 'message.received'
+
 ```
 
 **Universal hook events** -- these are defined by the spec and must be supported by all bindings:
@@ -1170,8 +1175,14 @@ hooks {
 | `matcher` | string | no | -- |
 | `run` | string | yes | -- |
 | `type` | hook-type | no | `command` |
+| `flag` | env-name | no (mod only) | -- |
 | `timeout` | number | no | `600` |
 
+A `type: mod` hook is a TypeScript module loaded inside the engine (Claude
+Code function hooks). Its `on:` is an `engine-event` (V95); a command or
+prompt hook takes a PascalCase event. `flag:` names the env variable that
+switches the Mod on. Fields are one per line (V90).
+
 ---
 
 ### 4.17 `settings`
@@ -1351,6 +1362,10 @@ agent processor {
 
 ---
 
+### 4.20a `file:` — hand-written internals
+
+Any node (`agent`, `group`, `human`, ...), any `skill` and any trigger `command` may carry `file: "<project-relative path>"`. It says: the structure is described here, the internals live in that file, and they are the author's. A binding never generates or overwrites a file so marked; for a skill it leaves the whole skill folder alone, for a group its skill and runtime folder too. Gates and hooks still wire to the node by name. `agentopology import` sets `file:` on every file it finds that no scaffold manifest lists as generated, which is what makes import followed by scaffold lossless.
+
 ### 4.21 `skill` (declarations)
 
 Topology-level skill declarations. Each `skill` block declares a self-contained application that bundles executable scripts, domain knowledge, reference docs, and instructions into a coherent capability. Agents load skills via their `skills` field.
@@ -1364,6 +1379,7 @@ skill-fields    = ('description' ':' string
                   | 'domains' ':' path-list
                   | 'references' ':' path-list
                   | 'prompt' ':' string
+                  | 'prompt' '{' text '}'
                   | 'disable-model-invocation' ':' boolean
                   | 'user-invocable' ':' boolean
                   | 'context' ':' identifier
@@ -1394,11 +1410,12 @@ skill classification {
 
 | Field | Type | Required | Default |
 |-------|------|----------|---------|
+| `file` | string | no | -- |
 | `description` | string | no | -- |
 | `scripts` | name-list | no | `[]` |
 | `domains` | path-list | no | `[]` |
 | `references` | path-list | no | `[]` |
-| `prompt` | string | no | -- |
+| `prompt` | string or block | no | -- |
 | `disable-model-invocation` | boolean | no | -- |
 | `user-invocable` | boolean | no | -- |
 | `context` | identifier | no | -- |
@@ -1406,6 +1423,8 @@ skill classification {
 | `allowed-tools` | tool-list | no | `[]` |
 | `extensions` | skill-extensions | no | -- |
 
+A skill's `prompt { }` block is its SKILL.md instructions; `prompt: "path"` names a file holding them, and the SKILL.md tells Claude to read and follow it.
+
 **`disable-model-invocation`** -- When `true`, prevents the skill from automatically invoking the model. Useful for skills that only run scripts.
 
 **`user-invocable`** -- When `true`, the skill appears in user-facing menus and can be triggered directly.

package/spec/testing.md

@@ -0,0 +1,85 @@
+# Testing spec: what the suite proves
+
+Every guarantee has an id. A test carries that id in its name (`[G3] ...`), and
+`src/__tests__/spec-testing-sync.test.ts` fails when an id here has no test, or
+a test names an id that isn't here. Open findings are listed as `it.todo` in
+`src/__tests__/open-findings.test.ts`, so the suite shows what is not yet
+guaranteed instead of hiding it.
+
+## How to run
+
+| Suite | Command | Needs |
+|---|---|---|
+| Everything offline (unit, CLI, e2e) | `npx vitest run` | nothing; the build runs first (vitest globalSetup), so tests never see a stale `dist/` |
+| Live Claude Code | `AT_LIVE=1 npx vitest run src/__tests__/live` | the `claude` CLI; one small haiku call per project; `AT_CLAUDE_BIN` overrides the binary |
+
+Run the live suite before every release, and after any change to a binding.
+
+## Guarantees
+
+| Id | Guarantee | Where |
+|---|---|---|
+| G1 | The first scaffold keeps a file it did not create (conflict, kept unless `--force`) | e2e/scaffold-owns.test.ts |
+| G2 | Scaffold never writes or deletes through a symlink, even with `--force` | e2e/scaffold-owns.test.ts |
+| G3 | Re-scaffolding keeps the user's hooks, `ask`, `defaultMode` and other permission keys | e2e/scaffold-owns.test.ts |
+| G4 | A second scaffold with no changes writes nothing | e2e/scaffold-owns.test.ts |
+| G5 | `--dry-run` writes nothing | e2e/scaffold-owns.test.ts |
+| G6 | Prose in a gate's `run` fails validate (V96) and scaffold, and nothing is written | e2e/scaffold-owns.test.ts |
+| G7 | An edited file that scaffold owns is kept on the next run | e2e/scaffold-owns.test.ts |
+| G8 | `--prune` removes untouched leftovers and keeps edited ones | e2e/scaffold-owns.test.ts |
+| G9 | Two topologies in one project keep separate manifests | e2e/scaffold-owns.test.ts |
+| G10 | No `${…}` reference or `#`-key reaches settings `env` (Claude Code applies env literally) | e2e/scaffold-owns.test.ts |
+| C1 | `scaffold --dry-run` lists, key by key, what a config merge would add or change in settings.json and .mcp.json | e2e/scaffold-owns.test.ts |
+| G11 | An unsafe generated path aborts the run before any file is written | scaffold/__tests__/safety.test.ts |
+| G12 | A second scaffold of an imported project changes nothing | e2e/roundtrip.test.ts |
+| G13 | An agent's `extensions` never leak into project-wide settings (only a topology-level `extensions` block is top-level) | e2e/roundtrip.test.ts |
+| G14 | An imported hook and its compiled form (`$CLAUDE_PROJECT_DIR`) merge as one hook, not two | e2e/roundtrip.test.ts |
+| G15 | V97 refuses a `file:` outside the project | e2e/roundtrip.test.ts |
+| G16 | Scaffold names every hand-written `file:` the project lacks | e2e/roundtrip.test.ts |
+| G17 | V11 does not demand a flow path for an on-demand (`invocation: manual`) agent | e2e/roundtrip.test.ts |
+| R1 | Import then scaffold keeps every hand-built file (was: 37 of 72 missing) | e2e/roundtrip.test.ts |
+| R2 | Import then scaffold leaves every hand-built file byte-identical, settings.json included (was: 2,957 lines cut to 1,706) | e2e/roundtrip.test.ts |
+| R3 | The imported .at validates with no errors (was: 22) | e2e/roundtrip.test.ts |
+| R4 | Import keeps frontmatter the language has no field for, comma-string lists, and the real `permissions` block | e2e/roundtrip.test.ts |
+| A4 | Agents, groups, skills and commands found on disk are imported with `file:` and never generated | e2e/roundtrip.test.ts |
+| F3 | `--allow-invalid` compiles despite validation errors; `--force` only overwrites kept files | e2e/roundtrip.test.ts |
+| C5 | A hook's own script is created only when missing: never overwritten (even with `--force`), reported or claimed | e2e/roundtrip.test.ts |
+| N4 | A url MCP server gets `type: http` (Claude Code skipped it) | e2e/compile.test.ts |
+| N5 | A `type: prompt` hook compiles to a prompt handler, in settings and in agent frontmatter | e2e/compile.test.ts |
+| N6 | Universal hook events map to Claude Code events (AgentStop → SubagentStop; Stop inside an agent) | e2e/compile.test.ts |
+| N7 | MCP names convert in whole-server, wildcard and dotted forms, in tools and in permission rules | e2e/compile.test.ts |
+| N8 | `permissions: confirm` and `bypass` compile to real `permissionMode` values; an unknown value is never emitted | e2e/compile.test.ts |
+| N9 | A regex hook matcher stays a valid YAML string in agent frontmatter | e2e/compile.test.ts |
+| N10 | A manual agent keeps its description (Claude Code skips an agent without one) | e2e/compile.test.ts |
+| N14 | `settings.ask` rules are emitted | e2e/compile.test.ts |
+| N17 | A scalar YAML would read as another type (`yes`, `1.0`) is quoted | e2e/compile.test.ts |
+| N19 | Scaffold output is byte-stable: no date in any generated file | e2e/compile.test.ts |
+| C3 | A `run:` line's script is the word after its interpreter, never an argument; a project script runs in place, from the project root | e2e/compile.test.ts |
+| C4 | A gate after an action or a human runs before its next agent launches (PreToolUse on the Agent tool; exit 2 blocks) | e2e/compile.test.ts |
+| H1 | A human node compiles to an approval step: Claude Code asks before launching the next agent, and the playbook says to ask; no ignored AGENT.md | e2e/compile.test.ts |
+| L4 | Real Claude Code blocks launching an agent when its gate fails, and stops at its approval step when the gate passes | live/claude-code.live.test.ts |
+| C2 | The topology context is written to `.claude/rules/<topology>.md`, never a CLAUDE.md, so it never competes with the project's own | e2e/compile.test.ts |
+| L5 | Real Claude Code loads the topology context from `.claude/rules/<topology>.md` | live/claude-code.live.test.ts |
+| N12 | A skill's instructions reach the model: a `prompt { }` block is the SKILL.md body; `prompt: "path"` tells Claude to read and follow the file | e2e/compile.test.ts |
+| A3 | An action's `commands:` are emitted whatever its kind; a non-inline action without commands is a marked stub that fails | e2e/compile.test.ts |
+| A3b | A tool's stub goes where its `script:` points (create-only for a project path), never a copy beside it | e2e/compile.test.ts |
+| B4 | A schedule runs headless from the project root, calls the real action path, and `every:` converts to cron (or warns) | e2e/compile.test.ts |
+| N21 | A `gate`, `hook`, `tool`, `job`, `command` or `level` outside its container block is a V98 error, never dropped silently | e2e/compile.test.ts |
+| N18 | An agent's `skills:`/`mcp-servers:` or a skill's `agent:` naming nothing declared is a V99 warning | e2e/compile.test.ts |
+| N16 | A model id Claude Code does not have is omitted with a warning; aliases, `inherit` and `claude-*` ids pass | e2e/compile.test.ts |
+| N11 | scaffold → sync is a fixed point: no edits leave the .at byte-identical; an edit between the prompt markers comes back once; re-scaffold keeps it | e2e/sync-cycle.test.ts |
+| L2 | Real Claude Code loads a hand-built project after import then scaffold | live/claude-code.live.test.ts |
+| L3 | Real Claude Code registers a manual agent and an agent with a regex matcher, and runs a prompt hook | live/claude-code.live.test.ts |
+| L1 | Real Claude Code loads every scaffolded example: every agent, skill and command registers, and the session succeeds | live/claude-code.live.test.ts |
+
+## Open findings (not yet guaranteed)
+
+Each is an `it.todo` with the same id. When one is fixed, its todo becomes a
+real test and the row moves to Guarantees. Source: the compile audit,
+2026-10-28/29 (plan page and `.history/2026-10-28-content-harness-gaps.md`).
+
+| Id | Finding | Phase |
+|---|---|---|
+| B5 | An agent's permissions read as per-agent grants; Claude Code allow rules are session-wide | 4 |
+| F1 | Missing first-class fields: agent effort, initialPrompt, omitClaudeMd, cache TTL, color; skill when_to_use, arguments, paths, shell | 4 |
+| F2 | Hooks as a typed union (http, mcp_tool, agent; once, async, if) | 4 |