@aligndottech/cli 0.57.0 → 0.58.0

package/dist/lib/model-cache.js

@@ -4,6 +4,7 @@
  */
 import { createHash } from 'node:crypto';
 import { existsSync, readFileSync } from 'node:fs';
+import { homedir } from 'node:os';
 import { join } from 'node:path';
 import { ensurePrivateDir, writePrivateFile } from './private-files.js';
 /**
@@ -32,4 +33,29 @@ export function modelFileCache(dir) {
         },
     };
 }
+/**
+ * Where everything the on-device embedding path caches lives: the model files and the native
+ * runtime, for the npm install and the standalone binary alike (one directory to warm in CI,
+ * one to delete to start clean).
+ *
+ * Never inside the install tree. transformers.js defaulted to `node_modules/@huggingface/
+ * transformers/.cache`, which is read-only for a root-owned global prefix (`sudo npm i -g`),
+ * is wiped by every upgrade, and ignored XDG_CACHE_HOME.
+ *
+ * `ALIGN_MODEL_CACHE` overrides all of it. Otherwise XDG_CACHE_HOME (or ~/.cache), and
+ * %LOCALAPPDATA% on Windows.
+ */
+export function modelCacheDir(env = process.env, platform = process.platform, home = homedir()) {
+    // Absolute only. The cache holds code the CLI loads (the native runtime), so a relative value,
+    // which a repo's .env can supply, would make the current repo's files the thing that gets loaded.
+    const override = env['ALIGN_MODEL_CACHE'];
+    if (override && /^(\/|[A-Za-z]:[\\/]|\\\\)/.test(override))
+        return override;
+    if (platform === 'win32') {
+        const base = env['LOCALAPPDATA'] || join(home, 'AppData', 'Local');
+        return join(base, 'align-cli', 'models');
+    }
+    const base = env['XDG_CACHE_HOME'] || join(home, '.cache');
+    return join(base, 'align-cli', 'models');
+}
 //# sourceMappingURL=model-cache.js.map

package/dist/lib/model-cache.js.map

@@ -1 +1 @@
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package/dist/lib/next-step.d.ts

@@ -33,6 +33,8 @@ export declare function orderAgents(w: WiredAgents): string[];
 export declare function projectAgentsFromWritten(written: string[]): string[];
 /** Prints only when something was actually wired: a connection claim with nothing behind it is worse than silence. */
 export declare function agentConnectedLine(agents: string[]): string | undefined;
+/** The first title in the list that makes a grammatical question, as it was given. */
+export declare function pickAskableTitle(titles: readonly string[]): string | undefined;
 /**
  * The question to hand the agent. Against a REAL decision the wizard found when there is one,
  * because "why did we X" is checkable against the repo the user is sitting in. The fallback

package/dist/lib/next-step.d.ts.map

@@ -1 +1 @@
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package/dist/lib/next-step.js

@@ -31,21 +31,43 @@ export function agentConnectedLine(agents) {
     return `Your agent is connected: ${agents.join(', ')}.`;
 }
 /**
- * A decision title is only safe to drop into "why did we X?" when X reads as an action
- * phrase (what WAS decided), not when it already reads as its own policy statement (what
- * MUST happen). "why did we All PRs must pass typecheck...?" is not a sentence - the title
- * was the rule, not the topic. Heuristic, not a parser: a handful of quantifier/modal
- * openers plus a length cap catch the real failure (ALI-934 preview QA, 2026-09-11) without
- * needing to understand the title's grammar.
+ * ALI-1779: a decision title is only quoted into "why did we X?" when X is a base-form verb
+ * phrase, so the result is a sentence. A raw commit subject is not one: "fix: error throwing in
+ * reply (#6299)" has a conventional prefix and a PR number, and "Improved links to MADR" is past
+ * tense. The prefix and PR number are stripped, and the rest must open with a verb from the list
+ * below; anything else (noun phrases, past tense, a leftover colon, policy statements such as
+ * "All PRs must ...", over twelve words) falls back to the generic question. The list is
+ * deliberately short and quoting a subject is optional, so a miss costs only a generic question.
  */
-const POLICY_STATEMENT_OPENERS = /^(all|every|no|never|always|nobody|everyone)\b/i;
+const CONVENTIONAL_PREFIX = /^(?:feat|fix|refactor|perf|types?|deps?|security)(?:\([^)]*\))?!?:\s*/i;
+const PR_REFERENCE = /\s*\(#\d+[^)]*\)/g;
 const MAX_TOPIC_WORDS = 12;
-function looksLikeTopic(title) {
-    if (POLICY_STATEMENT_OPENERS.test(title.trim()))
-        return false;
-    if (title.trim().split(/\s+/).length > MAX_TOPIC_WORDS)
-        return false;
-    return true;
+const BASE_VERBS = new Set([
+    'add', 'adopt', 'allow', 'avoid', 'change', 'close', 'consolidate', 'delegate', 'deprecate',
+    'disable', 'drop', 'enable', 'enforce', 'ensure', 'extract', 'fix', 'handle', 'ignore', 'implement',
+    'introduce', 'keep', 'make', 'migrate', 'move', 'prefer', 'prevent', 'put', 'refactor',
+    'reject', 'remove', 'rename', 'replace', 'require', 'restrict', 'reuse', 'send',
+    'simplify', 'skip', 'split', 'stop', 'switch', 'throw', 'treat', 'update',
+    'upgrade', 'use', 'validate', 'warn',
+]);
+/** The quotable phrase inside a commit subject or decision title, or undefined. */
+function askablePhrase(title) {
+    if (!title)
+        return undefined;
+    const phrase = title.trim().replace(CONVENTIONAL_PREFIX, '').replace(PR_REFERENCE, '').trim().replace(/\.$/, '');
+    if (phrase === '' || /[:?;#]/.test(phrase))
+        return undefined;
+    const words = phrase.split(/\s+/);
+    if (words.length > MAX_TOPIC_WORDS)
+        return undefined;
+    const verb = words[0].toLowerCase();
+    if (!BASE_VERBS.has(verb))
+        return undefined;
+    return verb + phrase.slice(words[0].length);
+}
+/** The first title in the list that makes a grammatical question, as it was given. */
+export function pickAskableTitle(titles) {
+    return titles.find((t) => askablePhrase(t) !== undefined);
 }
 /**
  * The question to hand the agent. Against a REAL decision the wizard found when there is one,
@@ -55,9 +77,8 @@ function looksLikeTopic(title) {
  * list tool rather than a similarity search.
  */
 export function firstQuestion(firstTitle) {
-    return firstTitle && looksLikeTopic(firstTitle)
-        ? `why did we ${firstTitle}?`
-        : 'what decisions exist in this codebase?';
+    const phrase = askablePhrase(firstTitle);
+    return phrase ? `why did we ${phrase}?` : 'what decisions exist in this codebase?';
 }
 /** Runnable AS PRINTED: bare `align mcp --setup` wires the cloud default, which is not a local user's graph. */
 function mcpSetupCommand(envName) {

package/dist/lib/next-step.js.map

@@ -1 +1 @@
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+{"version":3,"file":"next-step.js","sourceRoot":"","sources":["../../src/lib/next-step.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAuBhD;;;;GAIG;AACH,MAAM,UAAU,WAAW,CAAC,CAAc;IACxC,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,GAAG,GAAa,EAAE,CAAC;IACzB,KAAK,MAAM,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;QAC/C,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC;YAAE,SAAS;QAC7B,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACf,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACjB,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,wBAAwB,CAAC,OAAiB;IACxD,OAAO,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AAC9D,CAAC;AAED,sHAAsH;AACtH,MAAM,UAAU,kBAAkB,CAAC,MAAgB;IACjD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,SAAS,CAAC;IAC1C,OAAO,4BAA4B,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;AAC1D,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,mBAAmB,GAAG,wEAAwE,CAAC;AACrG,MAAM,YAAY,GAAG,mBAAmB,CAAC;AACzC,MAAM,eAAe,GAAG,EAAE,CAAC;AAC3B,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC;IACzB,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,UAAU,EAAE,WAAW;IAC3F,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,WAAW;IACnG,WAAW,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE,UAAU;IACtF,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,SAAS,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM;IAC/E,UAAU,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ;IACzE,SAAS,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM;CACrC,CAAC,CAAC;AAEH,mFAAmF;AACnF,SAAS,aAAa,CAAC,KAAyB;IAC9C,IAAI,CAAC,KAAK;QAAE,OAAO,SAAS,CAAC;IAC7B,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;IACjH,IAAI,MAAM,KAAK,EAAE,IAAI,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC;QAAE,OAAO,SAAS,CAAC;IAC7D,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;IAClC,IAAI,KAAK,CAAC,MAAM,GAAG,eAAe;QAAE,OAAO,SAAS,CAAC;IACrD,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE,CAAC;IACrC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,SAAS,CAAC;IAC5C,OAAO,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,MAAM,CAAC,CAAC;AAC/C,CAAC;AAED,sFAAsF;AACtF,MAAM,UAAU,gBAAgB,CAAC,MAAyB;IACxD,OAAO,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CAAC;AAC5D,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,aAAa,CAAC,UAA8B;IAC1D,MAAM,MAAM,GAAG,aAAa,CAAC,UAAU,CAAC,CAAC;IACzC,OAAO,MAAM,CAAC,CAAC,CAAC,cAAc,MAAM,GAAG,CAAC,CAAC,CAAC,wCAAwC,CAAC;AACrF,CAAC;AAED,gHAAgH;AAChH,SAAS,eAAe,CAAC,OAAgB;IACvC,OAAO,oBAAoB,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;AAChD,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,YAAY,CAAC,IAK5B;IACC,MAAM,QAAQ,GAAG,aAAa,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IAChD,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IAC7B,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,0BAA0B,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,kBAAkB,QAAQ,EAAE,CAAC;IAC7F,CAAC;IACD,OAAO,QAAQ,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,EAAE,aAAa,QAAQ,EAAE,CAAC;AACnF,CAAC;AAgCD,oEAAoE;AACpE,MAAM,WAAW,GAAG,EAAE,CAAC;AACvB,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;AACnC,CAAC;AAED,SAAS,SAAS,CAAC,CAAY;IAC7B,IAAI,CAAC,CAAC,IAAI,KAAK,OAAO,EAAE,CAAC;QACvB,MAAM,KAAK,GAAG,CAAC,CAAC,SAAS,KAAK,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,GAAG,GAAG,CAAC,GAAG,CAAC;QACjF,OAAO,GAAG,SAAS,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,eAAe,iCAAiC,KAAK,EAAE,CAAC;IAC/F,CAAC;IACD,MAAM,SAAS,GAAG,CAAC,CAAC,eAAe,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,eAAe,mBAAmB,CAAC,CAAC,CAAC,EAAE,CAAC;IACzF,OAAO,GAAG,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,SAAS,2BAA2B,SAAS,EAAE,CAAC;AACpF,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,mBAAmB,CAAC,IAAmB;IACrD,MAAM,KAAK,GAAG;QACZ,KAAK,IAAI,CAAC,SAAS,EAAE;QACrB,KAAK,SAAS,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,eAAe,EAAE;KAC3F,CAAC;IACF,IAAI,IAAI,CAAC,KAAK;QAAE,KAAK,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACzD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC;QACvB,yFAAyF;QACzF,KAAK,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC;QAC9C,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC;IAClC,CAAC;SAAM,CAAC;QACN,KAAK,CAAC,IAAI,CAAC,KAAK,YAAY,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,UAAU,EAAE,IAAI,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC;IAC9H,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC"}

package/dist/lib/node-floor.d.ts

@@ -0,0 +1,6 @@
+/**
+ * What to tell a person on a Node older than the floor, or null when the runtime is fine.
+ * Pure, and it must stay free of imports that reach node:sqlite: it runs before the CLI loads.
+ */
+export declare function nodeFloorMessage(version: string): string | null;
+//# sourceMappingURL=node-floor.d.ts.map

package/dist/lib/node-floor.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"node-floor.d.ts","sourceRoot":"","sources":["../../src/lib/node-floor.ts"],"names":[],"mappings":"AAEA;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAO/D"}

package/dist/lib/node-floor.js

@@ -0,0 +1,15 @@
+import { MIN_NODE, nodeMeetsFloor } from './doctor.js';
+/**
+ * What to tell a person on a Node older than the floor, or null when the runtime is fine.
+ * Pure, and it must stay free of imports that reach node:sqlite: it runs before the CLI loads.
+ */
+export function nodeFloorMessage(version) {
+    if (nodeMeetsFloor(version))
+        return null;
+    return [
+        `align needs Node ${MIN_NODE} or newer, and this is Node ${version}.`,
+        'Install a current Node from https://nodejs.org, open a new terminal, and run align again.',
+        'No Node to hand? The binary needs none: curl -fsSL https://align.tech/install.sh | sh',
+    ].join('\n');
+}
+//# sourceMappingURL=node-floor.js.map

package/dist/lib/node-floor.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"node-floor.js","sourceRoot":"","sources":["../../src/lib/node-floor.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAEvD;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAAC,OAAe;IAC9C,IAAI,cAAc,CAAC,OAAO,CAAC;QAAE,OAAO,IAAI,CAAC;IACzC,OAAO;QACL,oBAAoB,QAAQ,+BAA+B,OAAO,GAAG;QACrE,2FAA2F;QAC3F,uFAAuF;KACxF,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AACf,CAAC"}

package/dist/lib/safe-config-write.d.ts

@@ -1,4 +1,4 @@
-import { chmodSync, copyFileSync, lstatSync, mkdirSync, readdirSync, readFileSync, readlinkSync, renameSync, unlinkSync, writeFileSync } from 'node:fs';
+import { chmodSync, copyFileSync, lstatSync, mkdirSync, readdirSync, readFileSync, readlinkSync, renameSync, rmdirSync, unlinkSync, writeFileSync } from 'node:fs';
 export declare const BACKUP_SUFFIX = ".align-backup";
 export type SafeWriteStatus = 'written' | 'unchanged' | 'declined' | 'symlink';
 /** The fs calls the writer makes. A parameter so a test can change the file mid-write. */
@@ -13,6 +13,7 @@ export interface SafeFs {
     unlinkSync: typeof unlinkSync;
     mkdirSync: typeof mkdirSync;
     readdirSync: typeof readdirSync;
+    rmdirSync: typeof rmdirSync;
 }
 type Json = Record<string, unknown>;
 /** One value or array element align put in a JSON config. Hashes only, never the value. */
@@ -48,6 +49,11 @@ export interface WrittenConfig {
     /** 'made': align made the backup. 'foreign': one was already there and is not trusted. 'none': no original to keep. */
     backup: 'made' | 'foreign' | 'none';
     backupSha256?: string;
+    /**
+     * Where the backup lives when it is not beside the file (project files). Snapshots are
+     * `<backupAt>.<n>`. Absent: `<file>.align-backup`.
+     */
+    backupAt?: string;
     owned?: OwnedItem[];
     /**
      * Extra copies of the file taken just before a write that found it changed by someone else
@@ -57,6 +63,11 @@ export interface WrittenConfig {
         n: number;
         sha256: string;
     }>;
+    /**
+     * Directories align's first write made on the way to this file (outermost first). Undo removes
+     * each one only if it is empty by then, so a directory that held anything else stays.
+     */
+    createdDirs?: string[];
     /** Text files: the managed block align wrote. */
     block?: {
         start: string;
@@ -98,12 +109,24 @@ export interface SafeWriteOptions {
     };
     /** TOML only: the table (e.g. ['mcp_servers', 'align-local']) the managed block holds. */
     tomlTable?: string[];
+    /**
+     * A file in the user's repo, not in an agent's private config: new files and directories get the
+     * default mode (the umask decides) instead of owner-only, since a team shares them.
+     */
+    projectFile?: boolean;
     /** The tail of the invalid-JSON message: what to do about it. */
     invalidJsonAdvice?: string;
 }
 export declare class SafeWriteConflictError extends Error {
     constructor(file: string);
 }
+/**
+ * Where a PROJECT file's backup goes: `<state home>/align-cli/undo-backups/<sha of the full path>/<name>.align-backup`.
+ * Out of the repo on purpose, so nothing shows in `git status`. Keyed on the full path, the same key
+ * the ledger uses, so a moved repo loses both together and a same-named file elsewhere never collides.
+ * XDG_STATE_HOME is honoured; %LOCALAPPDATA% on Windows (case-folded there, as its paths are).
+ */
+export declare function projectBackupBase(file: string): string;
 /** The text form. `compute` gets the current text (null when missing) and returns the new text, or undefined to leave it. */
 export declare function safeWriteText(file: string, compute: (current: string | null) => string | undefined, opts?: SafeWriteOptions): SafeWriteStatus;
 /**

package/dist/lib/safe-config-write.d.ts.map

@@ -1 +1 @@
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package/dist/lib/safe-config-write.js

@@ -1,12 +1,15 @@
 import { createHash, randomBytes } from 'node:crypto';
-import { chmodSync, copyFileSync, lstatSync, mkdirSync, readdirSync, readFileSync, readlinkSync, renameSync, unlinkSync, writeFileSync, } from 'node:fs';
+import { chmodSync, copyFileSync, lstatSync, mkdirSync, readdirSync, readFileSync, readlinkSync, renameSync, rmdirSync, unlinkSync, writeFileSync, } from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { parse as parseToml } from 'smol-toml';
+import { stateHomeFor } from './backfill-state.js';
 /*
  * The one way align writes to a config file that belongs to someone else (an agent's MCP
  * config, its hook file). Promises, each of which a plain writeFileSync breaks:
- *  1. The FIRST content is kept in `<file>.align-backup` and never overwritten.
+ *  1. The FIRST content is kept in `<file>.align-backup` and never overwritten. A PROJECT file
+ *     (a committed AGENTS.md) is the exception: its copy goes under the user's state directory, so
+ *     `git status` shows nothing of it and `git add -A` cannot commit it.
  *  2. The file is re-read after our new content is staged. If another program changed it in
  *     the meantime we recompute once from what is there now, and give up if it moves again.
  *  3. The new content lands by an exclusive temp file + rename, keeping the old file's mode.
@@ -18,7 +21,7 @@ import { parse as parseToml } from 'smol-toml';
 export const BACKUP_SUFFIX = '.align-backup';
 // Built on use, not at import: a test that mocks node:fs with a few names must still be able
 // to import anything that reaches this module.
-const realFs = () => ({ readFileSync, writeFileSync, renameSync, copyFileSync, lstatSync, readlinkSync, chmodSync, unlinkSync, mkdirSync, readdirSync });
+const realFs = () => ({ readFileSync, writeFileSync, renameSync, copyFileSync, lstatSync, readlinkSync, chmodSync, unlinkSync, mkdirSync, readdirSync, rmdirSync });
 const isObject = (v) => typeof v === 'object' && v !== null && !Array.isArray(v);
 const sha = (data) => createHash('sha256').update(data).digest('hex');
 /** JSON with sorted keys, so a hash does not depend on key order. */
@@ -59,7 +62,9 @@ export function mergeWrittenConfig(prev, next) {
         firstSha256: prev.firstSha256,
         backup: prev.backup,
         ...(prev.backupSha256 ? { backupSha256: prev.backupSha256 } : {}),
+        ...(prev.backupAt ? { backupAt: prev.backupAt } : {}),
         ...(owned.size > 0 ? { owned: [...owned.values()] } : {}),
+        ...((prev.createdDirs?.length || next.createdDirs?.length) ? { createdDirs: [...new Set([...(prev.createdDirs ?? []), ...(next.createdDirs ?? [])])] } : {}),
         ...((prev.snapshots?.length || next.snapshots?.length) ? { snapshots: [...(prev.snapshots ?? []), ...(next.snapshots ?? [])] } : {}),
         ...(next.block
             ? { block: { ...next.block, ...(prev.block ? (prev.block.replaced ? { replaced: true } : {}) : next.block.replaced ? { replaced: true } : {}) } }
@@ -141,12 +146,15 @@ function modeOf(fs, file) {
     }
 }
 /** 'made' only when this call created the backup. Anything already at that path is not ours. */
-function backupOnce(fs, file) {
-    const backup = `${file}${BACKUP_SUFFIX}`;
+function backupOnce(fs, file, backup, private_) {
     if (linkAt(fs, backup) !== 'missing')
         return { state: 'foreign' };
+    if (private_)
+        fs.mkdirSync(path.dirname(backup), { recursive: true, mode: 0o700 });
     try {
         fs.copyFileSync(file, backup, 1); // COPYFILE_EXCL
+        if (private_)
+            fs.chmodSync(backup, 0o600);
     }
     catch (err) {
         if (err.code === 'EEXIST')
@@ -160,9 +168,11 @@ function backupOnce(fs, file) {
  * last write: the backup from before align's first write cannot hold what they added since.
  * `<file>.align-backup.<n>`, exclusive, 0600 (it may hold secrets), never overwritten.
  */
-function takeSnapshot(fs, file, content, taken) {
+function takeSnapshot(fs, file, base, content, taken) {
+    if (base !== `${file}${BACKUP_SUFFIX}`)
+        fs.mkdirSync(path.dirname(base), { recursive: true, mode: 0o700 });
     for (let n = Math.max(0, ...taken) + 1; n <= MAX_SNAPSHOTS; n++) {
-        const target = `${file}${BACKUP_SUFFIX}.${n}`;
+        const target = `${base}.${n}`;
         if (linkAt(fs, target) !== 'missing')
             continue;
         try {
@@ -178,9 +188,9 @@ function takeSnapshot(fs, file, content, taken) {
     throw new Error(`${file} already has ${taken.length} snapshots from align. Run \`align use --undo\` to clear them, then try again.`);
 }
 /** Delete snapshots THIS call made (verified: a regular file whose hash is the one taken). */
-function dropSnapshots(fs, file, list) {
+function dropSnapshots(fs, base, list) {
     for (const { n, sha256: want } of list) {
-        const target = `${file}${BACKUP_SUFFIX}.${n}`;
+        const target = `${base}.${n}`;
         try {
             if (fs.lstatSync(target).isFile() && sha(fs.readFileSync(target)) === want)
                 fs.unlinkSync(target);
@@ -190,6 +200,17 @@ function dropSnapshots(fs, file, list) {
         }
     }
 }
+/**
+ * Where a PROJECT file's backup goes: `<state home>/align-cli/undo-backups/<sha of the full path>/<name>.align-backup`.
+ * Out of the repo on purpose, so nothing shows in `git status`. Keyed on the full path, the same key
+ * the ledger uses, so a moved repo loses both together and a same-named file elsewhere never collides.
+ * XDG_STATE_HOME is honoured; %LOCALAPPDATA% on Windows (case-folded there, as its paths are).
+ */
+export function projectBackupBase(file) {
+    const abs = path.resolve(file);
+    const key = sha(process.platform === 'win32' ? abs.toLowerCase() : abs).slice(0, 24);
+    return path.join(stateHomeFor(process.env, os.homedir(), process.platform), 'align-cli', 'undo-backups', key, `${path.basename(file)}${BACKUP_SUFFIX}`);
+}
 const MAX_SNAPSHOTS = 200;
 const STALE_TMP_MS = 60_000;
 /** A crash between staging and rename leaves `.<name>.<hex>.align-tmp`. Old ones are removed. */
@@ -211,12 +232,12 @@ function sweepStaleTemps(fs, file) {
     }
 }
 /** Stage `text` beside `file` and rename it over. Never leaves the temp file behind on failure. */
-function stageAndRename(fs, file, text, mode, beforeRename) {
+function stageAndRename(fs, file, text, mode, beforeRename, newMode = 0o600) {
     let tmp = '';
     for (let i = 0; i < 5; i++) {
         tmp = path.join(path.dirname(file), `.${path.basename(file)}.${randomBytes(4).toString('hex')}.align-tmp`);
         try {
-            fs.writeFileSync(tmp, text, { encoding: 'utf8', mode: mode ?? 0o600, flag: 'wx' });
+            fs.writeFileSync(tmp, text, { encoding: 'utf8', mode: mode ?? newMode, flag: 'wx' });
             break;
         }
         catch (err) {
@@ -360,6 +381,22 @@ function blockOf(before, next, markers, tomlTable) {
     }
     return { start: markers.start, end: markers.end, sha256: sha(region), ...(old !== null && old !== region ? { replaced: true } : {}), ...(table ? { table } : {}) };
 }
+/** The directories on the way to `dir` that do not exist yet, outermost first. */
+function missingDirs(fs, dir) {
+    const missing = [];
+    for (let d = dir;; d = path.dirname(d)) {
+        try {
+            fs.lstatSync(d);
+            break;
+        }
+        catch {
+            missing.unshift(d);
+        }
+        if (path.dirname(d) === d)
+            break;
+    }
+    return missing;
+}
 function safeWrite(file, compute, opts, describe) {
     const fs = opts.fs ?? realFs();
     const note = opts.note ?? ((l) => console.error(l));
@@ -371,7 +408,11 @@ function safeWrite(file, compute, opts, describe) {
         return 'symlink';
     }
     let backup = { state: 'none' };
+    // A file already recorded keeps the place its first backup went; a new project file gets a place outside the repo.
+    const backupAt = lookup?.(file)?.backupAt ?? (opts.projectFile ? projectBackupBase(file) : undefined);
+    const backupBase = backupAt ?? `${file}${BACKUP_SUFFIX}`;
     const snapshots = [];
+    let createdDirs = [];
     for (let attempt = 0; attempt < 2; attempt++) {
         const before = readCurrent(fs, file);
         const next = compute(before);
@@ -379,7 +420,10 @@ function safeWrite(file, compute, opts, describe) {
             return 'declined';
         if (next === before)
             return 'unchanged';
-        fs.mkdirSync(path.dirname(file), { recursive: true, mode: 0o700 });
+        const madeDirs = missingDirs(fs, path.dirname(file));
+        fs.mkdirSync(path.dirname(file), { recursive: true, mode: opts.projectFile ? 0o777 : 0o700 });
+        if (madeDirs.length > 0)
+            createdDirs = madeDirs;
         sweepStaleTemps(fs, file);
         const mode = modeOf(fs, file);
         // The first time align writes a file that exists, the original is kept. After that, if the file
@@ -389,18 +433,18 @@ function safeWrite(file, compute, opts, describe) {
         if (before !== null) {
             if (!prev) {
                 if (backup.state === 'none')
-                    backup = backupOnce(fs, file);
+                    backup = backupOnce(fs, file, backupBase, backupAt !== undefined);
             }
             else if (sha(before) !== prev.sha256 && !snapshots.some((x) => x.sha256 === sha(before))) {
-                snapshots.push(takeSnapshot(fs, file, before, [...(prev.snapshots ?? []).map((x) => x.n), ...snapshots.map((x) => x.n)]));
+                snapshots.push(takeSnapshot(fs, file, backupBase, before, [...(prev.snapshots ?? []).map((x) => x.n), ...snapshots.map((x) => x.n)]));
             }
         }
         let staged = false;
         try {
-            staged = stageAndRename(fs, file, next, mode, () => readCurrent(fs, file) === before);
+            staged = stageAndRename(fs, file, next, mode, () => readCurrent(fs, file) === before, opts.projectFile ? 0o666 : 0o600);
         }
         catch (err) {
-            dropSnapshots(fs, file, snapshots);
+            dropSnapshots(fs, backupBase, snapshots);
             throw err;
         }
         if (!staged)
@@ -423,7 +467,7 @@ function safeWrite(file, compute, opts, describe) {
             ...(block?.replaced ? [block.snapshot ?? 0] : []),
         ]);
         const kept = snapshots.filter((x) => referenced.has(x.n));
-        dropSnapshots(fs, file, snapshots.filter((x) => !referenced.has(x.n)));
+        dropSnapshots(fs, backupBase, snapshots.filter((x) => !referenced.has(x.n)));
         try {
             recorder?.(file, {
                 created: before === null,
@@ -431,7 +475,9 @@ function safeWrite(file, compute, opts, describe) {
                 firstSha256: sha(next),
                 backup: backup.state,
                 ...(backup.sha256 ? { backupSha256: backup.sha256 } : {}),
+                ...(backupAt ? { backupAt } : {}),
                 ...(kept.length > 0 ? { snapshots: kept } : {}),
+                ...(createdDirs.length > 0 ? { createdDirs } : {}),
                 ...owned,
                 ...(block ? { block } : {}),
             });
@@ -442,7 +488,7 @@ function safeWrite(file, compute, opts, describe) {
         }
         return 'written';
     }
-    dropSnapshots(fs, file, snapshots);
+    dropSnapshots(fs, backupBase, snapshots);
     throw new SafeWriteConflictError(file);
 }
 /** The text form. `compute` gets the current text (null when missing) and returns the new text, or undefined to leave it. */
@@ -492,12 +538,20 @@ export function ownedOf(before, after, prev = [], snapshot = 0) {
             return !ownsElement(here, h);
         });
     };
+    /**
+     * A container that is already in the file but that align's own earlier write made: its
+     * createdDepth, so an entry added to it now is still pruned with it. null when it was the user's.
+     */
+    const madeByAlign = (here) => {
+        const depths = prev.filter((i) => i.path.length > here.length && samePath(i.path.slice(0, here.length), here) && i.createdDepth <= here.length).map((i) => i.createdDepth);
+        return depths.length > 0 ? Math.min(...depths) : null;
+    };
     const walk = (b, a, p, created) => {
         for (const [k, av] of Object.entries(a)) {
             const here = [...p, k];
             const has = b !== undefined && Object.prototype.hasOwnProperty.call(b, k);
             const bv = has ? b[k] : undefined;
-            const createdAt = created ?? (has ? null : here.length);
+            const createdAt = created ?? (has ? madeByAlign(here) : here.length);
             if (has && shaOf(av) === shaOf(bv))
                 continue;
             if (isObject(av) && Object.keys(av).length > 0 && here.length < 2 && (!has || isObject(bv))) {
@@ -662,17 +716,13 @@ function removeOwned(cur, owned, originalOf, backupPath) {
 export function undoWrittenConfigs(manifest, fs = realFs()) {
     const report = { restored: [], removed: [], cleaned: [], skipped: [], done: [] };
     for (const [file, entry] of Object.entries(manifest)) {
-        const backupPath = `${file}${BACKUP_SUFFIX}`;
+        const backupPath = entry.backupAt ?? `${file}${BACKUP_SUFFIX}`;
         const link = linkAt(fs, file);
         if (link && link !== 'missing') {
             report.skipped.push(`${file}: it is a symlink to ${link.target}, left alone`);
             continue;
         }
         const cur = readCurrent(fs, file);
-        if (cur === null) {
-            report.done.push(file); // already gone: nothing of align's is left
-            continue;
-        }
         // Compare-and-swap: the agent may rewrite its own file (Gemini saves settings) between the read
         // above and our write. Re-read right before every destructive step; if it moved, touch nothing.
         const moved = () => {
@@ -704,6 +754,17 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
             }
         };
         const backupTrusted = () => snapText(0) !== null;
+        /** Directories align made for this file, innermost first, each only while empty. */
+        const dropDirs = () => {
+            for (const d of [...(entry.createdDirs ?? [])].reverse()) {
+                try {
+                    fs.rmdirSync(d);
+                }
+                catch {
+                    break; /* not empty (or gone): the outer ones hold it too */
+                }
+            }
+        };
         /** Only after a fully clean undo, and only copies that are still align's own. */
         const dropBackup = () => {
             for (const n of [0, ...(entry.snapshots ?? []).map((x) => x.n)]) {
@@ -713,13 +774,29 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
                 }
                 catch { /* gone */ }
             }
+            // The directory holding an out-of-repo copy: removed only while empty.
+            if (entry.backupAt) {
+                try {
+                    fs.rmdirSync(path.dirname(entry.backupAt));
+                }
+                catch { /* not empty, or gone */ }
+            }
         };
+        if (cur === null) {
+            dropBackup(); // already gone: nothing of align's is left, and its saved copy must not linger as a stale 'foreign' one
+            report.done.push(file);
+            continue;
+        }
         // Whole-file only when align wrote this file exactly once and nobody has touched it since.
-        if (sha(cur) === entry.sha256 && entry.firstSha256 === entry.sha256) {
+        // A file align wrote WHOLE (no block, no owned keys: a generated plugin or rule) and created is all
+        // align's even after a re-run with other content, as long as it still equals the last write.
+        const wholeAlign = entry.created && !entry.block && !(entry.owned && entry.owned.length > 0);
+        if (sha(cur) === entry.sha256 && (entry.firstSha256 === entry.sha256 || wholeAlign)) {
             if (entry.created) {
                 if (moved())
                     continue;
                 fs.unlinkSync(file);
+                dropDirs();
                 report.removed.push(file);
                 report.done.push(file);
                 continue;
@@ -741,6 +818,14 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
                 continue;
             }
         }
+        // The file is exactly what align wrote, so only the original is missing. A copy kept outside the repo
+        // can go missing (a cleaned state directory, a moved repo): say so and leave the file, rather than
+        // guess at what to take out. The record stays, so a restored copy lets undo run again.
+        const needsOriginal = !!entry.block?.replaced || (entry.owned ?? []).some((i) => i.replaced || i.removed) || (!entry.block && !(entry.owned && entry.owned.length > 0));
+        if (entry.backupAt && !entry.created && entry.backup === 'made' && !backupTrusted() && needsOriginal && sha(cur) === entry.sha256 && entry.firstSha256 === entry.sha256) {
+            report.skipped.push(`${file}: align's saved copy of the original (${backupPath}) is missing or changed, so align left the file as it is. Take align's lines out by hand`);
+            continue;
+        }
         // Surgical: only align's own entries, and the user's own values back where align overwrote them.
         const mention = entry.backup === 'foreign' ? `; ${backupPath} was not made by align, so it was not used` : '';
         let next;
@@ -834,11 +919,12 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
         }
         // A file align created that holds nothing but align's own content once that is out: remove it, as
         // an untouched one is.
-        if (entry.created && entry.owned && !entry.block && next.trim() === '{}') {
+        if (entry.created && ((entry.owned && !entry.block && next.trim() === '{}') || (entry.block && next.trim() === ''))) {
             if (moved())
                 continue;
             fs.unlinkSync(file);
             dropBackup();
+            dropDirs();
             report.removed.push(file);
             report.done.push(file);
             continue;
@@ -846,6 +932,7 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
         if (next !== cur && !stageAndRename(fs, file, next, modeOf(fs, file), () => !moved()))
             continue;
         dropBackup();
+        dropDirs();
         report.cleaned.push(file);
         report.done.push(file);
     }