@aligndottech/cli 0.48.0 → 0.50.0

package/dist/lib/mcp-sync.js

@@ -0,0 +1,183 @@
+/**
+ * L5: the MCP tool `align_sync({ action })` - what the background refresh is doing, start it now,
+ * or price the optional AI classification.
+ *
+ * What it does, and what it cannot:
+ * - `status`: per source, scope, last success, status, items last run, discussion pending and
+ *   skip counts, the manual-refresh note for Teams and the exact re-auth command for a refused
+ *   token, and how many stored items wait for their links. Never an item's title, text or URL.
+ * - `run`: starts the SAME detached child a person gets from `align sync --background` and returns
+ *   (Decision 9). A tool call never runs a bulk fetch in the MCP server's own process, and it
+ *   returns inside journey 5's 500 ms. A source already syncing, or being backfilled, is not
+ *   started twice.
+ * - `classify_estimate`: how many LLM calls typing the imported items would cost, and the command
+ *   for the PERSON to run. There is no action that classifies: spending stays with the human
+ *   (Decision 16). No LLM call is made, here or by the child `run` starts.
+ * - Connecting or re-authenticating needs a token only the person can supply: nothing here takes
+ *   one. The input schema is closed, so a `token` or `api_key` property is refused before anything runs.
+ */
+import { backfillDir, liveBackfills, pidAlive, readStatus, reserveSlot, statusPath } from './backfill-state.js';
+import { createConfigStore } from './config.js';
+import { BACKFILL_SOURCES } from './mcp-backfill.js';
+import { estimateClassify } from './sync/classify.js';
+import { scopeStatusHooks } from './scope-real.js';
+import { lockHolder } from './sync/lock.js';
+import { startSyncChild } from './sync/spawn-background.js';
+import { readRows } from './sync/sync-state.js';
+import { collectStatus, renderStatus, TEAMS_NOTE } from './sync/status.js';
+export const SYNC_TOOL = 'align_sync';
+export const SYNC_ACTIONS = ['status', 'run', 'classify_estimate'];
+const DEFAULT_ESTIMATE_ITEMS = 25;
+export const SYNC_TOOL_SCHEMA = {
+    name: SYNC_TOOL,
+    annotations: { readOnlyHint: false, destructiveHint: false },
+    description: 'Check on, or start, the refresh of the sources the user has ALREADY connected into the local graph on this machine. ' +
+        'action "status" says per source when it last synced, whether it needs the person to re-authenticate, and what is still waiting; use it when the user asks whether the graph is up to date or why something is missing. ' +
+        'action "run" starts a background refresh now (it only reads from the sources, makes no LLM calls, and returns at once). ' +
+        'action "classify_estimate" says what typing the imported items with the user\'s own AI key would cost, plus the command for the user to run; it cannot start that. ' +
+        'It never takes a token or key: for a source that is not connected, or whose saved token was refused, the reply gives the exact `align connect <source>` command for the user to run themselves. Do not ask the user to paste a token into the chat.',
+    inputSchema: {
+        type: 'object',
+        properties: {
+            action: { type: 'string', enum: [...SYNC_ACTIONS], description: 'What to do' },
+            source: { type: 'string', enum: [...BACKFILL_SOURCES], description: 'With "run": only this source. Default: every connected source' },
+            max: { type: 'integer', minimum: 1, maximum: 1000, description: 'With "classify_estimate": how many items the person would classify (default 25)' },
+        },
+        required: ['action'],
+        additionalProperties: false,
+    },
+};
+export function defaultSyncDeps(env) {
+    const dbPath = env.localDbPath;
+    if (!dbPath)
+        throw new Error('align_sync needs the local graph path, and this server has none configured.');
+    const config = createConfigStore();
+    const dir = backfillDir();
+    const status = {
+        dbPath, ...scopeStatusHooks(config),
+        isConnected: (id) => Boolean(config.getConnectorFields('local', id)?.['token']),
+        syncRunning: (id) => lockHolder(`sync-${id}`) !== undefined,
+        backfill: (id) => (dir ? readStatus(statusPath(dir, id)) : null),
+        backfillAlive: (s) => s.state === 'running' && pidAlive(s.pid),
+    };
+    return {
+        dbPath, status,
+        needsReauth: (id) => readRows(dbPath, id).some((r) => r.status === 'needs_reauth'),
+        syncRunning: status.syncRunning,
+        backfillRunning: (id) => dir !== null && liveBackfills(dir).some((s) => s.source === id),
+        reserve: (sources) => {
+            const dir = backfillDir();
+            if (dir === null)
+                return { ok: false, busy: sources };
+            const taken = [];
+            for (const s of sources) {
+                const r = reserveSlot(dir, s);
+                if (!r.ok) {
+                    for (const t of taken)
+                        t.release();
+                    return { ok: false, busy: [s] };
+                }
+                taken.push(r);
+            }
+            return { ok: true, release: () => { for (const t of taken)
+                    t.release(); } };
+        },
+        start: (sources) => startSyncChild(sources),
+        estimate: estimateClassify,
+    };
+}
+function isAction(v) {
+    return typeof v === 'string' && SYNC_ACTIONS.includes(v);
+}
+export async function runSyncTool(args, env, injected) {
+    const input = args ?? {};
+    const unknownKeys = Object.keys(input).filter((k) => k !== 'action' && k !== 'source' && k !== 'max');
+    if (unknownKeys.length) {
+        // Names the keys, never their values: a rejected token must not be echoed into the transcript it was typed into.
+        const names = unknownKeys.slice(0, 3).map((k) => JSON.stringify(k.slice(0, 16))).join(', ');
+        throw new Error(`${SYNC_TOOL} takes only "action", "source" and "max", and does not accept ${names}. ` +
+            'It never accepts a token or key: the person connects a source themselves with `align connect <source>`.');
+    }
+    const action = input['action'];
+    if (!isAction(action))
+        throw new Error(`${SYNC_TOOL} requires "action", one of: ${SYNC_ACTIONS.join(', ')}. Call it again with one of those.`);
+    const source = input['source'];
+    if (source !== undefined && (typeof source !== 'string' || !BACKFILL_SOURCES.includes(source))) {
+        throw new Error(`${SYNC_TOOL} "source" must be one of: ${BACKFILL_SOURCES.join(', ')}.`);
+    }
+    const max = input['max'];
+    if (max !== undefined && (typeof max !== 'number' || !Number.isInteger(max) || max < 1 || max > 1000)) {
+        throw new Error(`${SYNC_TOOL} "max" must be a whole number from 1 to 1000.`);
+    }
+    if (env.mode !== 'local-embedded') {
+        throw new Error(`${SYNC_TOOL} refreshes the local graph on this machine, and this server reads a hosted Align graph. ` +
+            'Use the local Align server (align mcp --env local); a hosted graph is refreshed by its connectors.');
+    }
+    const d = injected ?? defaultSyncDeps(env);
+    switch (action) {
+        case 'status': {
+            const r = collectStatus(d.status);
+            return { text: renderStatus(r), sources: r.sources.filter((s) => s.connected), rows_awaiting_relink: r.rows_awaiting_relink };
+        }
+        case 'run':
+            return runAction(typeof source === 'string' ? source : undefined, d);
+        case 'classify_estimate': {
+            const e = d.estimate(d.dbPath, typeof max === 'number' ? max : DEFAULT_ESTIMATE_ITEMS);
+            if (e.available === 0)
+                return { text: 'Nothing to classify: no imported item has a close match that is still untyped.', available: 0 };
+            if (e.provider === undefined) {
+                return {
+                    text: `${e.available} imported items could be typed, but no AI provider is configured, so there is no estimate. Ask the person to run: align ai`,
+                    available: e.available,
+                };
+            }
+            return {
+                text: `Typing ${e.items} of ${e.available} imported items would use up to ${e.calls} LLM calls on your ${e.provider} key. Nothing was sent. To do it, ask the person to run: align sync --classify --max ${e.items}`,
+                available: e.available, items: e.items, max_llm_calls: e.calls, command: `align sync --classify --max ${e.items}`,
+            };
+        }
+    }
+}
+async function runAction(source, d) {
+    const connected = BACKFILL_SOURCES.filter((s) => d.status.isConnected(s));
+    const wanted = source !== undefined ? [source] : connected.filter((s) => s !== 'teams');
+    if (source !== undefined && !d.status.isConnected(source)) {
+        return { started: false, text: `${source} is not connected, so nothing was started. Connecting needs a token only the person can supply. Ask them to run: align connect ${source}` };
+    }
+    if (source === 'teams') {
+        return { started: false, text: `${TEAMS_NOTE} Nothing was started. Ask the person to run: align connect teams` };
+    }
+    if (wanted.length === 0) {
+        return { started: false, text: 'No source is connected, so there is nothing to refresh. Ask the person to run: align connect <source>' };
+    }
+    const reauth = wanted.filter((s) => d.needsReauth(s));
+    const busy = wanted.filter((s) => !reauth.includes(s) && (d.syncRunning(s) || d.backfillRunning(s)));
+    const go = wanted.filter((s) => !reauth.includes(s) && !busy.includes(s));
+    const notes = [];
+    if (reauth.length)
+        notes.push(`${reauth.join(', ')} ${reauth.length === 1 ? 'needs' : 'need'} the person to re-authenticate (the provider refused the saved token); ask them to run: ${reauth.map((s) => `align connect ${s}`).join(' ; ')}.`);
+    if (busy.length)
+        notes.push(`${busy.join(', ')} ${busy.length === 1 ? 'is' : 'are'} already syncing or being backfilled, so nothing new was started for ${busy.length === 1 ? 'it' : 'them'}.`);
+    if (go.length === 0)
+        return { started: false, text: notes.join(' ') };
+    const slot = d.reserve?.(go) ?? { ok: true, release: () => { } };
+    if (!slot.ok) {
+        return { started: false, text: `${slot.busy.join(', ')} ${slot.busy.length === 1 ? 'is' : 'are'} already being started or backfilled, so nothing new was started. ${notes.join(' ')}`.trim() };
+    }
+    let started;
+    try {
+        started = await d.start(go);
+    }
+    finally {
+        slot.release();
+    }
+    if (!started.ok) {
+        return { started: false, text: `The background process could not start, so nothing was started. The person can run it themselves: align sync ${go.join(' ')}`.trim() };
+    }
+    return {
+        started: true,
+        sources: go,
+        text: `Refresh started for ${go.join(', ')}. It runs in the background on this machine, only reads, and makes no LLM calls. Call ${SYNC_TOOL} with action "status" to see how it is going.${notes.length ? ` ${notes.join(' ')}` : ''}`,
+    };
+}
+//# sourceMappingURL=mcp-sync.js.map

package/dist/lib/mcp-sync.js.map

@@ -0,0 +1 @@
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package/dist/lib/personal-import.d.ts

@@ -18,6 +18,13 @@ export declare function runPersonalImport(items: PersonalImportItem[], client: R
         env: EnvironmentConfig;
         source: string;
     };
+    /** L3: filled with what the gateway STORED and how many batches failed, so the capture report
+     *  can say "imported 20 of 40 (a batch failed)" instead of the fetched count. Untouched when
+     *  the import throws or the process exits before ingest: the caller treats absence as unknown. */
+    result?: {
+        stored?: number;
+        failedBatches?: number;
+    };
 }): Promise<number>;
 /** A single confirm-each candidate: whatever it is, it can render itself for review. */
 export interface ConfirmEachItem {

package/dist/lib/personal-import.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"personal-import.d.ts","sourceRoot":"","sources":["../../src/lib/personal-import.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,eAAe,EAAE,mBAAmB,EAAE,MAAM,qBAAqB,CAAC;AAChF,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAGrD,MAAM,MAAM,kBAAkB,GAAG,eAAe,CAAC;AAoDjD,wBAAsB,kBAAkB,CAAC,CAAC,EACxC,KAAK,EAAE,KAAK,CAAC,MAAM,OAAO,CAAC,CAAC,CAAC,CAAC,EAC9B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,CAAC,CAYpC;AAED,wBAAsB,iBAAiB,CACrC,KAAK,EAAE,kBAAkB,EAAE,EAC3B,MAAM,EAAE,UAAU,CAAC,OAAO,mBAAmB,CAAC,EAC9C,IAAI,EAAE;IACJ,KAAK,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,OAAO,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,eAAe,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAC9G,mGAAmG;IACnG,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB;;4EAEwE;IACxE,MAAM,CAAC,EAAE;QAAE,GAAG,EAAE,iBAAiB,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;CACrD,GACA,OAAO,CAAC,MAAM,CAAC,CAoIjB;AAED,wFAAwF;AACxF,MAAM,WAAW,eAAe;IAC9B,MAAM,IAAI,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB;6DACyD;IACzD,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;;GASG;AACH,wBAAsB,oBAAoB,CAAC,CAAC,SAAS,eAAe,EAClE,KAAK,EAAE,CAAC,EAAE,EACV,QAAQ,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,OAAO,CAAC;IAAE,EAAE,EAAE,MAAM,CAAA;CAAE,CAAC,EAC9C,IAAI,EAAE;IAAE,KAAK,EAAE,MAAM,CAAA;CAAE,GACtB,OAAO,CAAC,iBAAiB,CAAC,CAiC5B"}
+{"version":3,"file":"personal-import.d.ts","sourceRoot":"","sources":["../../src/lib/personal-import.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,eAAe,EAAE,mBAAmB,EAAE,MAAM,qBAAqB,CAAC;AAChF,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAGrD,MAAM,MAAM,kBAAkB,GAAG,eAAe,CAAC;AAoDjD,wBAAsB,kBAAkB,CAAC,CAAC,EACxC,KAAK,EAAE,KAAK,CAAC,MAAM,OAAO,CAAC,CAAC,CAAC,CAAC,EAC9B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,CAAC,CAYpC;AAED,wBAAsB,iBAAiB,CACrC,KAAK,EAAE,kBAAkB,EAAE,EAC3B,MAAM,EAAE,UAAU,CAAC,OAAO,mBAAmB,CAAC,EAC9C,IAAI,EAAE;IACJ,KAAK,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,OAAO,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,eAAe,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAC9G,mGAAmG;IACnG,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB;;4EAEwE;IACxE,MAAM,CAAC,EAAE;QAAE,GAAG,EAAE,iBAAiB,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;IACpD;;sGAEkG;IAClG,MAAM,CAAC,EAAE;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,aAAa,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC;CACtD,GACA,OAAO,CAAC,MAAM,CAAC,CA2IjB;AAED,wFAAwF;AACxF,MAAM,WAAW,eAAe;IAC9B,MAAM,IAAI,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB;6DACyD;IACzD,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;;GASG;AACH,wBAAsB,oBAAoB,CAAC,CAAC,SAAS,eAAe,EAClE,KAAK,EAAE,CAAC,EAAE,EACV,QAAQ,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,OAAO,CAAC;IAAE,EAAE,EAAE,MAAM,CAAA;CAAE,CAAC,EAC9C,IAAI,EAAE;IAAE,KAAK,EAAE,MAAM,CAAA;CAAE,GACtB,OAAO,CAAC,iBAAiB,CAAC,CAiC5B"}

package/dist/lib/personal-import.js

@@ -69,6 +69,10 @@ export async function runWithConcurrency(tasks, concurrency) {
     return results;
 }
 export async function runPersonalImport(items, client, opts) {
+    if (opts.result) {
+        opts.result.stored = 0;
+        opts.result.failedBatches = 0;
+    }
     if (!items.length) {
         if (!opts.silent)
             p.log.warn(`No items found from ${opts.label}.`);
@@ -111,9 +115,13 @@ export async function runPersonalImport(items, client, opts) {
     let done = 0;
     const failures = [];
     const spinner = opts.quiet ? null : ora(`Importing 0/${batches.length} batches...`).start();
+    // L1: classify:false on every batch. Every caller of this function is a connector import,
+    // and the local client otherwise runs the paid classifier on up to 3 candidates per item
+    // whenever a provider key is exported. Explicit human capture (captureDecision) keeps it.
+    // keyed: true marks these as connector imports, the only rows that get a source_key. The cloud client ignores both.
     const results = await runWithConcurrency(batches.map((batch) => async () => {
         try {
-            return await ingestBatchResilient(() => client.ingestBatch(batch, { deferEnrichment: opts.deferEnrichment }));
+            return await ingestBatchResilient(() => client.ingestBatch(batch, { deferEnrichment: opts.deferEnrichment, classify: false, keyed: true }));
         }
         finally {
             done++;
@@ -143,6 +151,10 @@ export async function runPersonalImport(items, client, opts) {
             failures.push(`Batch ${i + 1}: ${r.reason.message}`);
         }
     }
+    if (opts.result) {
+        opts.result.stored = total;
+        opts.result.failedBatches = failures.length;
+    }
     // ALI-795: ingest ran (the empty-items case returned above), so the funnel stage
     // fires whichever rendering branch follows. Consent gating lives in the emitter.
     // No await (Copilot on #215): never-throws, and the completion line must not wait

package/dist/lib/personal-import.js.map

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

@@ -61,9 +61,18 @@ export interface WrittenConfig {
     block?: {
         start: string;
         end: string;
-        sha256: string; /** a block was already there, and align's replaced it: the original is in the backup */
+        sha256: string;
+        /** a block was already there, and align's replaced it: the original is in the backup */
         replaced?: boolean;
         snapshot?: number;
+        /**
+         * TOML only: the one table the block holds, and the hash of its parsed value. Lets undo take
+         * that table out when another program re-serialised the file and dropped the markers.
+         */
+        table?: {
+            path: string[];
+            sha256: string;
+        };
     };
 }
 /** Fold one write into what the manifest already holds for that file. */
@@ -87,6 +96,8 @@ export interface SafeWriteOptions {
         start: string;
         end: string;
     };
+    /** TOML only: the table (e.g. ['mcp_servers', 'align-local']) the managed block holds. */
+    tomlTable?: string[];
     /** The tail of the invalid-JSON message: what to do about it. */
     invalidJsonAdvice?: string;
 }

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

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

@@ -2,6 +2,7 @@ import { createHash, randomBytes } from 'node:crypto';
 import { chmodSync, copyFileSync, lstatSync, mkdirSync, readdirSync, readFileSync, readlinkSync, renameSync, unlinkSync, writeFileSync, } from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
+import { parse as parseToml } from 'smol-toml';
 /*
  * 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:
@@ -242,17 +243,122 @@ function stageAndRename(fs, file, text, mode, beforeRename) {
         throw err;
     }
 }
+/**
+ * The managed block: the start marker and the NEXT end marker after it. null when it is missing,
+ * and also when it is ambiguous (a second start, or an end before the start): a region guessed
+ * across someone else's lines would take them out with it.
+ */
 function regionOf(text, markers) {
     const s = text.indexOf(markers.start);
-    const e = text.indexOf(markers.end);
-    return s === -1 || e === -1 || e < s ? null : text.slice(s, e + markers.end.length);
+    if (s === -1)
+        return null;
+    const e = text.indexOf(markers.end, s + markers.start.length);
+    if (e === -1)
+        return null;
+    if (text.indexOf(markers.start, s + 1) !== -1)
+        return null;
+    const firstEnd = text.indexOf(markers.end);
+    if (firstEnd !== -1 && firstEnd < s)
+        return null;
+    return text.slice(s, e + markers.end.length);
 }
-function blockOf(before, next, markers) {
+function getAt(root, p) {
+    let node = root;
+    for (const k of p) {
+        if (!isObject(node) || !Object.hasOwn(node, k))
+            return undefined;
+        node = node[k];
+    }
+    return node;
+}
+/** A TOML table header for exactly `path` (bare, "quoted" or 'quoted' keys, spaces around dots). */
+function tomlHeader(p) {
+    const esc = (k) => k.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+    const key = (k) => `(?:${esc(k)}|"${esc(k)}"|'${esc(k)}')`;
+    return new RegExp(`^[ \\t]*\\[[ \\t]*${p.map(key).join('[ \\t]*\\.[ \\t]*')}[ \\t]*\\][ \\t]*(?:#.*)?$`, 'gm');
+}
+/**
+ * Take one table align added out of a TOML file whose markers another program removed (Grok
+ * Build re-serialises config.toml on `grok mcp add`). Only when the table is exactly what align
+ * wrote, appears once as a header, and taking its lines out changes nothing else in the parsed
+ * file. Returns the new text, or a line saying what to remove by hand.
+ */
+function removeTomlTable(cur, table) {
+    const name = `[${table.path.join('.')}]`;
+    let before;
+    try {
+        before = parseToml(cur);
+    }
+    catch {
+        return { why: `align's marked block is gone and the file is not valid TOML now; remove the ${name} table by hand` };
+    }
+    const value = getAt(before, table.path);
+    if (value === undefined)
+        return { text: cur };
+    if (shaOf(value) !== table.sha256)
+        return { why: `align's marked block is gone and ${name} was changed since align added it; remove the ${name} table by hand` };
+    const headers = [...cur.matchAll(tomlHeader(table.path))];
+    if (headers.length !== 1)
+        return { why: `align's marked block is gone and align cannot find exactly one ${name} header; remove the ${name} table by hand` };
+    const from = headers[0].index;
+    const rest = cur.slice(from + headers[0][0].length);
+    const nextHeader = /^[ \t]*\[/m.exec(rest);
+    const to = nextHeader ? from + headers[0][0].length + nextHeader.index : cur.length;
+    // The cut must hold align's table lines and nothing else: no comment (a note the user put there
+    // would go with it), no blank line inside the table, at most one blank line after it.
+    const body = cur.slice(from + headers[0][0].length, to).replace(/^\n/, '').split('\n');
+    if (body[body.length - 1] === '')
+        body.pop();
+    let trailing = 0;
+    while (trailing < body.length && body[body.length - 1 - trailing].trim() === '')
+        trailing += 1;
+    const inner = body.slice(0, body.length - trailing);
+    if (headers[0][0].includes('#') || inner.some((l) => l.trim() === '' || l.includes('#')) || trailing > 1) {
+        return { why: `align's marked block is gone and other lines sit inside or around ${name}; remove the ${name} table by hand` };
+    }
+    const next = `${cur.slice(0, from)}${cur.slice(to)}`.replace(/\n{3,}/g, '\n\n');
+    const expected = JSON.parse(JSON.stringify(before));
+    const parent = getAt(expected, table.path.slice(0, -1));
+    if (isObject(parent))
+        delete parent[table.path[table.path.length - 1]];
+    let after;
+    try {
+        after = parseToml(next);
+    }
+    catch {
+        after = undefined;
+    }
+    // An emptied parent table may or may not survive in the text: compare with it gone on both sides.
+    const prune = (o) => {
+        const pp = table.path.slice(0, -1);
+        const node = getAt(o, pp);
+        const holder = getAt(o, pp.slice(0, -1));
+        if (pp.length > 0 && isObject(node) && Object.keys(node).length === 0 && isObject(holder))
+            delete holder[pp[pp.length - 1]];
+        return o;
+    };
+    if (after === undefined || shaOf(prune(after)) !== shaOf(prune(expected))) {
+        return { why: `align's marked block is gone and align cannot take ${name} out without touching your other settings; remove it by hand` };
+    }
+    return { text: next };
+}
+function blockOf(before, next, markers, tomlTable) {
     const region = regionOf(next, markers);
     if (region === null)
         return undefined;
     const old = before === null ? null : regionOf(before, markers);
-    return { start: markers.start, end: markers.end, sha256: sha(region), ...(old !== null && old !== region ? { replaced: true } : {}) };
+    let table;
+    if (tomlTable) {
+        try {
+            const value = getAt(parseToml(region.slice(markers.start.length)), tomlTable);
+            if (value !== undefined)
+                table = { path: tomlTable, sha256: shaOf(value) };
+        }
+        catch {
+            // No table record: a lost block is then skipped by undo, never guessed at.
+        }
+    }
+    return { start: markers.start, end: markers.end, sha256: sha(region), ...(old !== null && old !== region ? { replaced: true } : {}), ...(table ? { table } : {}) };
 }
 function safeWrite(file, compute, opts, describe) {
     const fs = opts.fs ?? realFs();
@@ -306,7 +412,7 @@ function safeWrite(file, compute, opts, describe) {
         let block;
         try {
             owned = describe?.(lastSnap) ?? {};
-            const b = opts.markers ? blockOf(before, next, opts.markers) : undefined;
+            const b = opts.markers ? blockOf(before, next, opts.markers, opts.tomlTable) : undefined;
             block = b ? { ...b, ...(b.replaced ? { snapshot: lastSnap } : {}) } : undefined;
         }
         catch {
@@ -567,6 +673,19 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
             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 = () => {
+            let now = null;
+            try {
+                now = readCurrent(fs, file);
+            }
+            catch { /* unreadable counts as moved */ }
+            if (now === cur)
+                return false;
+            report.skipped.push(`${file}: it changed while undo was running, so align left it as it is now. Run \`align use --undo\` again`);
+            return true;
+        };
         // The first backup (0) and the snapshots (1..n): each is trusted only when it is a regular file
         // whose hash is the one align recorded when it made it.
         const snapPath = (n) => (n === 0 ? backupPath : `${backupPath}.${n}`);
@@ -598,6 +717,8 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
         // 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) {
             if (entry.created) {
+                if (moved())
+                    continue;
                 fs.unlinkSync(file);
                 report.removed.push(file);
                 report.done.push(file);
@@ -606,6 +727,13 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
             if (backupTrusted()) {
                 const tmp = path.join(path.dirname(file), `.${path.basename(file)}.${randomBytes(4).toString('hex')}.align-tmp`);
                 fs.copyFileSync(backupPath, tmp, 1);
+                if (moved()) {
+                    try {
+                        fs.unlinkSync(tmp);
+                    }
+                    catch { /* gone */ }
+                    continue;
+                }
                 fs.renameSync(tmp, file);
                 dropBackup();
                 report.restored.push(file);
@@ -619,8 +747,18 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
         const left = [];
         if (entry.block) {
             const region = regionOf(cur, entry.block);
-            if (region === null)
-                next = cur;
+            if (region === null) {
+                // The block is gone or ambiguous: another program rewrote the file, or the user edited it.
+                // Never "cleaned" on a guess: take out a recorded TOML table only when it is provably
+                // align's, otherwise keep the record and the backup and say what to remove.
+                const r = entry.block.table ? removeTomlTable(cur, entry.block.table) : { why: `align's marked block (${entry.block.start} ... ${entry.block.end}) is no longer intact in the file, so align cannot tell what to take out. Remove what align added there by hand` };
+                if ('text' in r)
+                    next = r.text;
+                else {
+                    next = cur;
+                    left.push(r.why);
+                }
+            }
             else if (sha(region) !== entry.block.sha256) {
                 next = cur;
                 left.push('the block align manages was edited since align wrote it; remove it by hand');
@@ -670,6 +808,19 @@ export function undoWrittenConfigs(manifest, fs = realFs()) {
             };
             left.push(...removeOwned(parsed, entry.owned, originalOf, backupPath));
             next = JSON.stringify(parsed, null, 2) + (cur.endsWith('\n') ? '\n' : '');
+            // Once align's entries are out, a file that means exactly what the original meant gets the
+            // original's bytes back (align's own refreshes made the whole-file path unavailable, and a
+            // re-serialisation would change the user's formatting).
+            const original = snapText(0);
+            if (original !== null && left.length === 0) {
+                try {
+                    if (JSON.stringify(JSON.parse(original)) === JSON.stringify(parsed))
+                        next = original;
+                }
+                catch {
+                    // the original is not JSON: keep the re-serialised text
+                }
+            }
         }
         else {
             report.skipped.push(`${file}: align has no record of what it added here. Remove its entries by hand${mention}`);
@@ -684,14 +835,16 @@ 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 (moved())
+                continue;
             fs.unlinkSync(file);
             dropBackup();
             report.removed.push(file);
             report.done.push(file);
             continue;
         }
-        if (next !== cur)
-            stageAndRename(fs, file, next, modeOf(fs, file));
+        if (next !== cur && !stageAndRename(fs, file, next, modeOf(fs, file), () => !moved()))
+            continue;
         dropBackup();
         report.cleaned.push(file);
         report.done.push(file);