agentopology 0.5.2 → 0.7.0

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

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+/**
+ * Scaffold changes only what it owns.
+ *
+ * Found compiling a real harness (content-harness.at, 2026-10-28): the first
+ * scaffold skipped the plan and wrote every file, so it would have overwritten
+ * six hand-written SKILL.md files, settings.json, .mcp.json and a crontab —
+ * two of the skills through symlinks into another repository — and then
+ * crashed on a junk path with no manifest left behind.
+ */
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import * as fs from "node:fs";
+import * as path from "node:path";
+import * as os from "node:os";
+import { hashContent } from "../manifest.js";
+import { computeIncrementalPlan, executeActions, nextManifestFiles, unsafePathReason, } from "../incremental.js";
+import { parse } from "../../parser/index.js";
+import { validate } from "../../parser/validator.js";
+import { proseInRun, scriptNameFromRun } from "../../parser/run.js";
+import { claudeCodeBinding } from "../../bindings/claude-code.js";
+let dir;
+beforeEach(() => {
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), "at-safety-"));
+});
+afterEach(() => {
+    fs.rmSync(dir, { recursive: true, force: true });
+});
+const put = (rel, content) => {
+    fs.mkdirSync(path.dirname(path.join(dir, rel)), { recursive: true });
+    fs.writeFileSync(path.join(dir, rel), content, "utf-8");
+};
+const read = (rel) => fs.readFileSync(path.join(dir, rel), "utf-8");
+const manifestOf = (files) => ({
+    source: "t.at", sourceHash: "x", target: "claude-code", generatedAt: "", files,
+});
+describe("first scaffold never overwrites a file it did not create", () => {
+    it("plans an existing hand-written skill as a conflict and keeps it", () => {
+        put(".claude/skills/story/SKILL.md", "REAL SKILL");
+        const files = [
+            { path: ".claude/skills/story/SKILL.md", content: "stub", category: "machine" },
+            { path: ".claude/agents/a/AGENT.md", content: "agent", category: "agent" },
+        ];
+        const actions = computeIncrementalPlan(dir, "claude-code", files, null);
+        expect(actions.map((a) => a.type)).toEqual(["conflict", "create"]);
+        const result = executeActions(dir, actions, { prune: false, force: false });
+        expect(read(".claude/skills/story/SKILL.md")).toBe("REAL SKILL");
+        expect(read(".claude/agents/a/AGENT.md")).toBe("agent");
+        // The kept file is never claimed, so a later --prune cannot delete it.
+        const owned = nextManifestFiles(dir, actions, files, null, result);
+        expect(Object.keys(owned)).toEqual([".claude/agents/a/AGENT.md"]);
+    });
+    it("overwrites it only with --force", () => {
+        put("CLAUDE.md", "mine");
+        const files = [{ path: "CLAUDE.md", content: "generated", category: "machine" }];
+        const actions = computeIncrementalPlan(dir, "claude-code", files, null);
+        executeActions(dir, actions, { prune: false, force: true });
+        expect(read("CLAUDE.md")).toBe("generated");
+    });
+});
+describe("symlinks are never written or deleted through", () => {
+    it("blocks a file under a linked folder, even with --force", () => {
+        const elsewhere = fs.mkdtempSync(path.join(os.tmpdir(), "at-other-repo-"));
+        fs.writeFileSync(path.join(elsewhere, "SKILL.md"), "OTHER REPO");
+        fs.mkdirSync(path.join(dir, ".claude/skills"), { recursive: true });
+        fs.symlinkSync(elsewhere, path.join(dir, ".claude/skills/the-book"));
+        const files = [
+            { path: ".claude/skills/the-book/SKILL.md", content: "stub", category: "machine" },
+        ];
+        const actions = computeIncrementalPlan(dir, "claude-code", files, null);
+        expect(actions[0].type).toBe("blocked");
+        executeActions(dir, actions, { prune: false, force: true });
+        expect(fs.readFileSync(path.join(elsewhere, "SKILL.md"), "utf-8")).toBe("OTHER REPO");
+        fs.rmSync(elsewhere, { recursive: true, force: true });
+    });
+});
+describe("an unsafe path aborts the run before anything is written", () => {
+    it.each([
+        [".claude/skills/t/scripts/", "ends in '/'"],
+        [".claude/skills/t/scripts/E;", "unsafe name"],
+        [".claude/skills/t/scripts/fail:", "unsafe name"],
+        [".claude/skills/t/scripts/outputs.py)", "unsafe name"],
+        ["../escape.sh", "climbs out"],
+        ["/etc/passwd", "absolute"],
+    ])("refuses %s", (p, why) => {
+        expect(unsafePathReason(p)).toContain(why);
+    });
+    it("[G11] writes none of the good files when one path is bad", () => {
+        const files = [
+            { path: "good.md", content: "x", category: "machine" },
+            { path: ".claude/skills/t/scripts/", content: "x", category: "script" },
+        ];
+        const actions = computeIncrementalPlan(dir, "claude-code", files, null);
+        expect(() => executeActions(dir, actions, { prune: false, force: true })).toThrow(/unsafe path/);
+        expect(fs.existsSync(path.join(dir, "good.md"))).toBe(false);
+    });
+});
+describe("re-scaffold keeps edits to files scaffold owns", () => {
+    it("treats an edited CLAUDE.md as a conflict, not an update", () => {
+        put(".claude/CLAUDE.md", "generated\nmy own note\n");
+        const manifest = manifestOf({ ".claude/CLAUDE.md": { hash: hashContent("generated\n"), category: "machine" } });
+        const files = [{ path: ".claude/CLAUDE.md", content: "generated v2\n", category: "machine" }];
+        const actions = computeIncrementalPlan(dir, "claude-code", files, manifest);
+        expect(actions[0]).toMatchObject({ type: "conflict", detail: "user edited" });
+    });
+    it("updates an untouched owned file", () => {
+        put(".claude/CLAUDE.md", "generated\n");
+        const manifest = manifestOf({ ".claude/CLAUDE.md": { hash: hashContent("generated\n"), category: "machine" } });
+        const files = [{ path: ".claude/CLAUDE.md", content: "generated v2\n", category: "machine" }];
+        expect(computeIncrementalPlan(dir, "claude-code", files, manifest)[0].type).toBe("update");
+    });
+});
+describe("--prune deletes only what scaffold left untouched", () => {
+    it("keeps an edited leftover and removes a clean one with its empty folder", () => {
+        put(".claude/agents/old/AGENT.md", "as generated");
+        put(".claude/agents/edited/AGENT.md", "as generated + my edits");
+        const manifest = manifestOf({
+            ".claude/agents/old/AGENT.md": { hash: hashContent("as generated"), category: "agent" },
+            ".claude/agents/edited/AGENT.md": { hash: hashContent("as generated"), category: "agent" },
+        });
+        const actions = computeIncrementalPlan(dir, "claude-code", [], manifest);
+        executeActions(dir, actions, { prune: true, force: true });
+        expect(fs.existsSync(path.join(dir, ".claude/agents/old"))).toBe(false);
+        expect(read(".claude/agents/edited/AGENT.md")).toBe("as generated + my edits");
+    });
+});
+describe("prose in run (V96)", () => {
+    // Real values from content-harness.at.
+    const prose = [
+        "auto_gates.py: G1 truth, G2 vendor, G3 credit",
+        "pxframes gate mean >= 3.85, no frame < 3; pooled 3 runs",
+        "frames 0.0 / 0.5 / 3.0 s differ",
+        "BUILT 10-28 (ME-R76): kit.py --at 'YYYY-MM-DD HH:MM'",
+        "vowel_check.py (BUILT 10-28, ME-535) -> the LISTEN LIST",
+    ];
+    const commands = [
+        "scripts/check-quality.sh",
+        "./media validate --step all",
+        "python3 docs/content-os/gift.py run",
+        "bash -c 'echo (quoted) ok'",
+        "test -f out.json && jq '.ok' out.json",
+        ".claude/scripts/log-subagent.sh",
+        "/opt/homebrew/bin/python3 ./harness-plugin/hooks/router.py --flag",
+    ];
+    it.each(prose)("flags %s", (r) => expect(proseInRun(r)).not.toBeNull());
+    it.each(commands)("accepts %s", (r) => expect(proseInRun(r)).toBeNull());
+    it("keeps the historical script name for real commands", () => {
+        expect(scriptNameFromRun("scripts/check-quality.sh")).toBe("check-quality.sh");
+        expect(scriptNameFromRun("frames 0.0 / 0.5 / 3.0 s differ")).toBeNull();
+    });
+    const example = fs.readFileSync(path.join(__dirname, "../../../examples/simple-pipeline.at"), "utf-8");
+    const at = (run) => example.replace('run: "scripts/check-quality.sh"', `run: "${run}"`);
+    it("validate rejects it, and the binding emits no junk path even when forced", () => {
+        const ast = parse(at("pxframes gate mean >= 3.85, no frame < 3; frames 0.0 / 0.5 / 3.0 s"));
+        expect(validate(ast).some((r) => r.rule === "V96" && r.level === "error")).toBe(true);
+        const files = claudeCodeBinding.scaffold(ast);
+        expect(files.filter((f) => unsafePathReason(f.path))).toEqual([]);
+    });
+    it("a real command still compiles to its script and hook", () => {
+        const ast = parse(at("scripts/check.sh"));
+        expect(validate(ast).filter((r) => r.rule === "V96")).toEqual([]);
+        const paths = claudeCodeBinding.scaffold(ast).map((f) => f.path);
+        expect(paths).toContain(".claude/skills/simple-pipeline/scripts/check.sh");
+        expect(paths).toContain(".claude/skills/simple-pipeline/scripts/gate-quality-check.sh");
+    });
+});
+describe("two topologies in one project keep separate manifests", () => {
+    it("does not treat another topology's files as its own", async () => {
+        const { readManifest, writeManifest } = await import("../manifest.js");
+        put("crontab.fragment", "0 * * * * other-topology\n");
+        writeManifest(dir, "claude-code", {
+            ...manifestOf({ "crontab.fragment": { hash: hashContent("0 * * * * other-topology\n"), category: "machine" } }),
+            source: "youtube-flywheel.at",
+        });
+        const mine = readManifest(dir, "claude-code", "content-harness.at");
+        expect(mine).toBeNull();
+        const files = [{ path: "crontab.fragment", content: "0 6 * * * mine\n", category: "machine" }];
+        const actions = computeIncrementalPlan(dir, "claude-code", files, mine);
+        expect(actions[0]).toMatchObject({ type: "conflict", detail: "exists, not created by scaffold" });
+        // Writing this topology's manifest leaves the other one in place.
+        writeManifest(dir, "claude-code", { ...manifestOf({}), source: "content-harness.at" });
+        expect(readManifest(dir, "claude-code", "youtube-flywheel.at")?.files["crontab.fragment"]).toBeDefined();
+        expect(readManifest(dir, "claude-code", "content-harness.at")).not.toBeNull();
+    });
+});
+//# sourceMappingURL=safety.test.js.map

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

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

@@ -231,11 +231,12 @@ describe("computeIncrementalPlan", () => {
             source: "t.at", sourceHash: "x", target: "claude-code",
             generatedAt: "", files: {
                 "keep.md": { hash: "abc", category: "machine" },
-                "removed.md": { hash: "def", category: "machine" },
+                "removed.md": { hash: hashContent("old output"), category: "machine" },
             },
         };
         const content = "kept";
         fs.writeFileSync(path.join(tmpDir, "keep.md"), content, "utf-8");
+        fs.writeFileSync(path.join(tmpDir, "removed.md"), "old output", "utf-8");
         const files = [
             { path: "keep.md", content, category: "machine" },
         ];

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

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

@@ -86,7 +86,7 @@ describe("Change 3 — deepMergeSettingsJson", () => {
         // Generated-only key added
         expect(merged.env.BAZ).toBe("added");
     });
-    it("hooks are REWRITTEN by generated (topology owns hooks)", () => {
+    it("hooks the topology owns are replaced; the user's are kept", () => {
         const existing = JSON.stringify({
             hooks: {
                 PreToolUse: [{ matcher: "old", hooks: [{ type: "command", command: "old.sh" }] }],
@@ -97,11 +97,14 @@ describe("Change 3 — deepMergeSettingsJson", () => {
                 SubagentStop: [{ matcher: "new", hooks: [{ type: "command", command: "new.sh" }] }],
             },
         });
-        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
-        // Old hooks gone — topology owns hooks
-        expect(merged.hooks.PreToolUse).toBeUndefined();
-        // New hooks present
-        expect(merged.hooks.SubagentStop).toBeDefined();
+        // old.sh is the topology's own script: its hook is replaced.
+        const owned = JSON.parse(deepMergeSettingsJson(existing, generated, ["old.sh"]));
+        expect(owned.hooks.PreToolUse).toBeUndefined();
+        expect(owned.hooks.SubagentStop).toBeDefined();
+        // Nothing claimed: old.sh is the user's hook and survives.
+        const user = JSON.parse(deepMergeSettingsJson(existing, generated));
+        expect(user.hooks.PreToolUse[0].hooks[0].command).toBe("old.sh");
+        expect(user.hooks.SubagentStop).toBeDefined();
     });
     it("preserves user-only top-level keys", () => {
         const existing = JSON.stringify({
@@ -140,7 +143,9 @@ describe("Change 3 — deepMergeSettingsJson", () => {
 // ---------------------------------------------------------------------------
 describe("settings.json merge is wired into the scaffold pipeline", () => {
     const settings = (obj) => JSON.stringify(obj, null, 2);
-    const plan = (existing, generated) => {
+    // `owned` lists scripts an earlier scaffold of this topology wrote: hooks
+    // that run them are the topology's; every other hook is the user's.
+    const plan = (existing, generated, owned = []) => {
         const dir = mkdtempSync(join(tmpdir(), "at-settings-"));
         const rel = ".claude/settings.json";
         mkdirSync(join(dir, ".claude"), { recursive: true });
@@ -153,7 +158,10 @@ describe("settings.json merge is wired into the scaffold pipeline", () => {
             sourceHash: "x",
             target: "claude-code",
             generatedAt: new Date().toISOString(),
-            files: { [rel]: { hash: hashContent(existing), category: "shared-config" } },
+            files: {
+                [rel]: { hash: hashContent(existing), category: "shared-config" },
+                ...Object.fromEntries(owned.map((p) => [p, { hash: "x", category: "script" }])),
+            },
         };
         const actions = computeIncrementalPlan(dir, "claude-code", generatedFiles, manifest);
         rmSync(dir, { recursive: true, force: true });
@@ -184,12 +192,35 @@ describe("settings.json merge is wired into the scaffold pipeline", () => {
             hooks: { SubagentStop: [{ matcher: "gone", hooks: [{ type: "command", command: "x.sh" }] }] },
         });
         const generated = settings({ permissions: { allow: ["Read"] } });
-        const action = plan(existing, generated);
+        const action = plan(existing, generated, ["x.sh"]);
         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");
     });
+    // A re-scaffold deleted every hook the user added by hand, and rebuilt
+    // permissions from allow/deny alone — ask and defaultMode vanished.
+    it("keeps the user's own hooks, ask rules and defaultMode on re-scaffold", () => {
+        const existing = settings({
+            permissions: { allow: ["Read"], ask: ["Bash(git push:*)"], defaultMode: "acceptEdits", additionalDirectories: ["../docs"] },
+            hooks: {
+                PreToolUse: [{ matcher: "Bash", hooks: [{ type: "command", command: "bash ./my-guard.sh" }] }],
+                SubagentStop: [{ matcher: "writer", hooks: [{ type: "command", command: "bash .claude/skills/t/scripts/gate-old.sh" }] }],
+            },
+        });
+        const generated = settings({
+            permissions: { allow: ["Write"] },
+            hooks: { SubagentStop: [{ matcher: "writer", hooks: [{ type: "command", command: "bash .claude/skills/t/scripts/gate-new.sh" }] }] },
+        });
+        const merged = JSON.parse(plan(existing, generated, [".claude/skills/t/scripts/gate-old.sh"]).content);
+        expect(merged.hooks.PreToolUse[0].hooks[0].command).toBe("bash ./my-guard.sh");
+        expect(JSON.stringify(merged.hooks.SubagentStop)).toContain("gate-new.sh");
+        expect(JSON.stringify(merged.hooks.SubagentStop)).not.toContain("gate-old.sh");
+        expect(merged.permissions.ask).toEqual(["Bash(git push:*)"]);
+        expect(merged.permissions.defaultMode).toBe("acceptEdits");
+        expect(merged.permissions.additionalDirectories).toEqual(["../docs"]);
+        expect(merged.permissions.allow).toEqual(["Read", "Write"]);
+    });
     it("still unions permissions the user added by hand", () => {
         const existing = settings({ permissions: { allow: ["Read", "MyOwnTool"] } });
         const generated = settings({ permissions: { allow: ["Read", "Write"] } });

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

@@ -1 +1 @@
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package/dist/scaffold/diff.d.ts

@@ -0,0 +1,17 @@
+/**
+ * What a config merge changes, key by key, for `scaffold --dry-run`.
+ *
+ * The dry run used to say only "config merged" for settings.json and
+ * .mcp.json, so the one file a user most needs to review before a write was
+ * the one it did not show (content session, 2026-10-29).
+ *
+ * @module
+ */
+/**
+ * Lines describing how `after` differs from `before`: `+ path: value` for an
+ * addition, `~ path: old → new` for a change, `- path` for a removal. Arrays
+ * are compared by element (an element present in only one side is added or
+ * removed), which is how the merge treats permission and hook lists.
+ */
+export declare function jsonChanges(beforeText: string, afterText: string): string[];
+//# sourceMappingURL=diff.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"diff.d.ts","sourceRoot":"","sources":["../../src/scaffold/diff.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAaH;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,MAAM,EAAE,CAgC3E"}

package/dist/scaffold/diff.js

@@ -0,0 +1,66 @@
+/**
+ * What a config merge changes, key by key, for `scaffold --dry-run`.
+ *
+ * The dry run used to say only "config merged" for settings.json and
+ * .mcp.json, so the one file a user most needs to review before a write was
+ * the one it did not show (content session, 2026-10-29).
+ *
+ * @module
+ */
+const MAX_VALUE = 120;
+function show(value) {
+    const text = JSON.stringify(value);
+    return text.length > MAX_VALUE ? `${text.slice(0, MAX_VALUE - 1)}…` : text;
+}
+function isObject(v) {
+    return typeof v === "object" && v !== null && !Array.isArray(v);
+}
+/**
+ * Lines describing how `after` differs from `before`: `+ path: value` for an
+ * addition, `~ path: old → new` for a change, `- path` for a removal. Arrays
+ * are compared by element (an element present in only one side is added or
+ * removed), which is how the merge treats permission and hook lists.
+ */
+export function jsonChanges(beforeText, afterText) {
+    let before;
+    let after;
+    try {
+        before = JSON.parse(beforeText);
+        after = JSON.parse(afterText);
+    }
+    catch {
+        return ["(not JSON: shown whole on write)"];
+    }
+    const out = [];
+    const walk = (a, b, path) => {
+        if (isObject(a) && isObject(b)) {
+            for (const key of new Set([...Object.keys(a), ...Object.keys(b)])) {
+                const p = path ? `${path}.${key}` : key;
+                if (!(key in a))
+                    out.push(`+ ${p}: ${show(b[key])}`);
+                else if (!(key in b))
+                    out.push(`- ${p}`);
+                else
+                    walk(a[key], b[key], p);
+            }
+            return;
+        }
+        if (Array.isArray(a) && Array.isArray(b)) {
+            const keyOf = (v) => JSON.stringify(v);
+            const had = new Set(a.map(keyOf));
+            const has = new Set(b.map(keyOf));
+            for (const v of b)
+                if (!had.has(keyOf(v)))
+                    out.push(`+ ${path}[]: ${show(v)}`);
+            for (const v of a)
+                if (!has.has(keyOf(v)))
+                    out.push(`- ${path}[]: ${show(v)}`);
+            return;
+        }
+        if (JSON.stringify(a) !== JSON.stringify(b))
+            out.push(`~ ${path}: ${show(a)} → ${show(b)}`);
+    };
+    walk(before, after, "");
+    return out;
+}
+//# sourceMappingURL=diff.js.map

package/dist/scaffold/diff.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"diff.js","sourceRoot":"","sources":["../../src/scaffold/diff.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,MAAM,SAAS,GAAG,GAAG,CAAC;AAEtB,SAAS,IAAI,CAAC,KAAc;IAC1B,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC;IACnC,OAAO,IAAI,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;AAC7E,CAAC;AAED,SAAS,QAAQ,CAAC,CAAU;IAC1B,OAAO,OAAO,CAAC,KAAK,QAAQ,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;AAClE,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,UAAkB,EAAE,SAAiB;IAC/D,IAAI,MAAe,CAAC;IACpB,IAAI,KAAc,CAAC;IACnB,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QAChC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,kCAAkC,CAAC,CAAC;IAC9C,CAAC;IACD,MAAM,GAAG,GAAa,EAAE,CAAC;IACzB,MAAM,IAAI,GAAG,CAAC,CAAU,EAAE,CAAU,EAAE,IAAY,EAAE,EAAE;QACpD,IAAI,QAAQ,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/B,KAAK,MAAM,GAAG,IAAI,IAAI,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;gBAClE,MAAM,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;gBACxC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;oBAAE,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;qBAChD,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;oBAAE,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;;oBACpC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;YAC/B,CAAC;YACD,OAAO;QACT,CAAC;QACD,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;YACzC,MAAM,KAAK,GAAG,CAAC,CAAU,EAAE,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;YAChD,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;YAClC,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;YAClC,KAAK,MAAM,CAAC,IAAI,CAAC;gBAAE,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;oBAAE,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,OAAO,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YAC/E,KAAK,MAAM,CAAC,IAAI,CAAC;gBAAE,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;oBAAE,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,OAAO,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YAC/E,OAAO;QACT,CAAC;QACD,IAAI,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC;YAAE,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;IAC9F,CAAC,CAAC;IACF,IAAI,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC;IACxB,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/scaffold/incremental.d.ts

@@ -1,19 +1,29 @@
 /**
  * Incremental scaffold orchestrator.
  *
- * Computes a plan of file actions (create, update, delete, unchanged, conflict)
- * by comparing freshly generated files against what is on disk and what was
- * previously tracked in the scaffold manifest.
+ * Computes a plan of file actions (create, update, delete, unchanged, conflict,
+ * blocked) by comparing freshly generated files against what is on disk and
+ * what was previously tracked in the scaffold manifest.
+ *
+ * The rule the plan enforces: scaffold only changes what it owns. A file is
+ * owned when the manifest records it. Anything else on disk — a hand-written
+ * skill, a settings file, a symlink into another repo — is a conflict (kept
+ * unless --force) or blocked (never touched). The first scaffold used to skip
+ * this plan and write everything; it overwrote real files and, following a
+ * symlink, files in a second repository.
  *
  * @module
  */
 import type { GeneratedFile } from "../bindings/types.js";
-import type { FileAction, ScaffoldManifest } from "./types.js";
+import type { FileAction, ManifestEntry, ScaffoldManifest } from "./types.js";
+export { unsafePathReason } from "../parser/paths.js";
 /**
  * Compute an incremental scaffold plan.
  *
  * Compares generated files against what exists on disk and the previous
- * manifest to determine the minimal set of file operations needed.
+ * manifest to determine the minimal set of file operations needed. Used for
+ * the first scaffold too (manifest null): every existing file is then
+ * unmanaged and therefore a conflict, never an overwrite.
  *
  * @param basePath - Absolute path to the project root
  * @param target - Binding target name (e.g. "claude-code")
@@ -22,22 +32,48 @@ import type { FileAction, ScaffoldManifest } from "./types.js";
  * @returns Array of file actions to execute
  */
 export declare function computeIncrementalPlan(basePath: string, target: string, generatedFiles: GeneratedFile[], manifest: ScaffoldManifest | null): FileAction[];
+/** Result of {@link executeActions}. */
+export interface ExecuteResult {
+    created: number;
+    updated: number;
+    deleted: number;
+    unchanged: number;
+    conflicts: number;
+    blocked: number;
+    /** Paths whose content on disk is now what this run wrote. */
+    written: Map<string, string>;
+    /** Paths removed from disk by this run. */
+    removed: string[];
+    /** Writes that failed; the run continues with the other files. */
+    failures: Array<{
+        path: string;
+        error: string;
+    }>;
+}
 /**
  * Execute a set of file actions against the filesystem.
  *
+ * Refuses outright when the plan holds an unsafe path, so a bad plan writes
+ * nothing at all. A single failed write is recorded and the rest proceed, so
+ * the caller can still write a manifest that matches the disk.
+ *
  * @param basePath - Absolute path to the project root
  * @param actions - File actions computed by {@link computeIncrementalPlan}
  * @param options - Execution options
- * @returns Counts of each action type performed
+ * @returns Counts of each action type performed, plus what was written
  */
 export declare function executeActions(basePath: string, actions: FileAction[], options: {
     prune: boolean;
     force: boolean;
-}): {
-    created: number;
-    updated: number;
-    deleted: number;
-    unchanged: number;
-    conflicts: number;
-};
+}): ExecuteResult;
+/**
+ * The manifest after a run: exactly the files scaffold now owns, hashed as
+ * they are on disk.
+ *
+ * Owned = written or unchanged this run, plus earlier entries for files the
+ * run left alone (an edited file keeps its old hash, so it stays a conflict;
+ * an unpruned leftover stays tracked, so a later --prune can still remove it).
+ * A pre-existing file scaffold did not write is never claimed.
+ */
+export declare function nextManifestFiles(basePath: string, actions: FileAction[], generatedFiles: GeneratedFile[], previous: ScaffoldManifest | null, result: ExecuteResult): Record<string, ManifestEntry>;
 //# sourceMappingURL=incremental.d.ts.map