@coderook/cli 0.32.1 → 0.33.1

package/.claude-plugin/plugin.json

@@ -2,7 +2,7 @@
   "name": "coderook",
   "displayName": "CodeRook",
   "description": "Save, browse and restore whole-snapshot versions of a project on CodeRook, from Claude Code.",
-  "version": "0.32.1",
+  "version": "0.33.1",
   "author": {
     "name": "ACCA Gaming Productions",
     "url": "https://coderook.com"

package/README.md

@@ -331,7 +331,7 @@ does not already have.
 | Tag kind | A lightweight tag comes back annotated. CodeRook records a name, not which sort of tag made it. |
 | Force pushes, branch deletion | Refused — versions are immutable, so there is nothing to rewind to. |
 | Submodules | Skipped on push, and it says which paths. |
-| The executable bit | Everything arrives as a normal file. A script cloned back needs `chmod +x`. |
+| The executable bit | Kept: a script pushed as `100755` clones back executable, with `cbx clone` and `git clone` alike. Versions saved before 0.33 recorded every file as not executable. |
 
 **On round trips.** Push then clone gives you back the same *files*, not the
 same *commit ids*. A commit id covers its author, committer and timestamps,

package/dist/cbx/src/core/download.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Downloader = exports.DownloadCancelled = void 0;
 exports.underway = underway;
+exports.applyMode = applyMode;
 /**
  * Bringing a project down: the file list for a version, then its bytes.
  *
@@ -18,6 +19,7 @@ const node_fs_1 = require("node:fs");
 const promises_1 = require("node:fs/promises");
 const promises_2 = require("node:stream/promises");
 const node_stream_1 = require("node:stream");
+const node_zlib_1 = require("node:zlib");
 const node_path_1 = __importDefault(require("node:path"));
 const safe_path_js_1 = require("../shared/safe_path.js");
 const identify_js_1 = require("./identify.js");
@@ -290,6 +292,7 @@ class Downloader {
                 ...(row.objectId ? { objectId: String(row.objectId) } : {}),
                 sha256: String(row.sha256 ?? ""),
                 sourceSize: Number(row.sourceSize ?? 0),
+                ...(row.executable === true ? { executable: true } : {}),
                 ...(row.sealed === true ? { sealed: true } : {}),
                 ...(packed?.objectId
                     ? {
@@ -344,7 +347,9 @@ class Downloader {
      */
     async fileTo(repositoryId, versionId, file, target) {
         await (0, promises_1.mkdir)(node_path_1.default.dirname(target), { recursive: true });
-        return this.fetchInto(repositoryId, versionId, file, target);
+        const digest = await this.fetchInto(repositoryId, versionId, file, target);
+        await applyMode(target, file.executable === true);
+        return digest;
     }
     /**
      * Reconstruct and verify every file in a Version without materialising the
@@ -489,6 +494,18 @@ class Downloader {
             await (0, promises_1.rm)(temporary, { force: true });
         }
     }
+    /*
+      Paths whose bytes arrived still gzip-compressed and were recovered.
+  
+      A service that recorded an object's encoding wrongly served its stored
+      gzip as though it were the file (found on CodeRook in September 2026; the
+      service now judges the encoding from the stored size). The bytes were
+      never damaged, only still compressed, so a body that fails its digest,
+      starts with gzip's magic number and decompresses to exactly the expected
+      digest is accepted. Anything else still fails. Listed here so a caller
+      can say it happened.
+    */
+    recoveredFromGzip = [];
     async fetchInto(repositoryId, versionId, file, target) {
         const whole = (0, node_crypto_1.createHash)("sha256");
         /*
@@ -499,6 +516,7 @@ class Downloader {
           that cannot match the digest this file was listed with.
         */
         const pieces = file.sealed ? [] : (file.chunks ?? []);
+        let recovered = false;
         // Captured so the generators below do not need `this` rebound.
         const request = (route) => this.request(route);
         const check = () => this.check();
@@ -508,7 +526,7 @@ class Downloader {
                     check();
                     const piece = pieces[at];
                     const reply = await request(`/v1/repositories/${repositoryId}/objects/${piece.objectId}`);
-                    const body = Buffer.from(await reply.arrayBuffer());
+                    let body = Buffer.from(await reply.arrayBuffer());
                     /*
                       Checked against what the upload recorded for this piece, before
                       a byte of it reaches the file. Without the digest the only
@@ -517,8 +535,13 @@ class Downloader {
                     */
                     const digest = (0, node_crypto_1.createHash)("sha256").update(body).digest("hex");
                     if (piece.sha256 && digest !== piece.sha256) {
-                        throw new Error(`${file.path}: piece ${at + 1} of ${pieces.length} ` +
-                            `did not arrive intact`);
+                        const plain = gunzippedMatching(body, piece.sha256);
+                        if (!plain) {
+                            throw new Error(`${file.path}: piece ${at + 1} of ${pieces.length} ` +
+                                `did not arrive intact`);
+                        }
+                        recovered = true;
+                        body = plain;
                     }
                     whole.update(body);
                     yield body;
@@ -545,7 +568,16 @@ class Downloader {
           up holding something that looks finished.
         */
         await (0, promises_2.pipeline)(source, (0, node_fs_1.createWriteStream)(target));
-        return whole.digest("hex");
+        const digest = whole.digest("hex");
+        if (recovered)
+            this.recoveredFromGzip.push(file.path);
+        if (!pieces.length && file.sha256 && digest !== file.sha256) {
+            if (await recoverGzipFile(target, file.sha256)) {
+                this.recoveredFromGzip.push(file.path);
+                return file.sha256;
+            }
+        }
+        return digest;
     }
     /**
      * Write a version into `destination`.
@@ -801,6 +833,7 @@ class Downloader {
                 await (0, promises_1.mkdir)(node_path_1.default.dirname(target), { recursive: true });
                 await (0, promises_1.rm)(target, { recursive: true, force: true });
                 await (0, promises_1.rename)((0, safe_path_js_1.inside)(staging, file.path), target);
+                await applyMode(target, file.executable === true);
                 placed += 1;
                 if (placed === 1)
                     (0, faults_js_1.maybeFail)("get:after-first-file");
@@ -849,3 +882,68 @@ class Downloader {
     }
 }
 exports.Downloader = Downloader;
+/** The gunzipped bytes when they hash to `expected`, otherwise null. */
+function gunzippedMatching(body, expected) {
+    if (body.length < 2 || body[0] !== 0x1f || body[1] !== 0x8b)
+        return null;
+    try {
+        const plain = (0, node_zlib_1.gunzipSync)(body);
+        return (0, node_crypto_1.createHash)("sha256").update(plain).digest("hex") === expected ? plain : null;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Replace a file that arrived still gzip-compressed with its contents, when
+ * those contents hash to `expected`. Streamed, so a large file is never held.
+ */
+async function recoverGzipFile(target, expected) {
+    const handle = await (0, promises_1.open)(target, "r");
+    const magic = Buffer.alloc(2);
+    try {
+        await handle.read(magic, 0, 2, 0);
+    }
+    finally {
+        await handle.close();
+    }
+    if (magic[0] !== 0x1f || magic[1] !== 0x8b)
+        return false;
+    const temporary = `${target}.gunzip`;
+    const hash = (0, node_crypto_1.createHash)("sha256");
+    try {
+        await (0, promises_2.pipeline)((0, node_fs_1.createReadStream)(target), (0, node_zlib_1.createGunzip)(), new node_stream_1.Transform({
+            transform(chunk, _encoding, done) {
+                hash.update(chunk);
+                done(null, chunk);
+            },
+        }), (0, node_fs_1.createWriteStream)(temporary));
+    }
+    catch {
+        await (0, promises_1.rm)(temporary, { force: true });
+        return false;
+    }
+    if (hash.digest("hex") !== expected) {
+        await (0, promises_1.rm)(temporary, { force: true });
+        return false;
+    }
+    await (0, promises_1.rename)(temporary, target);
+    return true;
+}
+/**
+ * Give a written file the execute bit its version records, or take it away.
+ *
+ * Windows has no execute bit, so nothing is done there. Elsewhere a script
+ * that came back as an ordinary file could not be run until somebody noticed
+ * and ran chmod, which on Linux was every shell script in every clone.
+ */
+async function applyMode(target, executable) {
+    if (process.platform === "win32")
+        return;
+    try {
+        await (0, promises_1.chmod)(target, executable ? 0o755 : 0o644);
+    }
+    catch {
+        /* A file that cannot take a mode is still the right file. */
+    }
+}

package/dist/cbx/src/core/upload.js

@@ -805,9 +805,19 @@ class Uploader {
                     sourceSize: held.sourceSize,
                     storedSize: held.storedSize,
                     mediaType: held.mediaType,
+                    executable: request.executable?.get(file.path) ?? held.executable,
                 };
             }),
         ].sort((left, right) => left.path.localeCompare(right.path));
+        /*
+          Whether each sent file runs. Every file used to go up as not, so a
+          script cloned on Linux came back unusable until somebody ran chmod.
+        */
+        for (const item of contents) {
+            if (item.executable !== undefined)
+                continue;
+            item.executable = await executableFor(request, item.path, prior.get(item.path)?.executable ?? false);
+        }
         /*
           Last check before the version is written: everything the person ticked
           has to be in it. Reaching this with something missing would publish a
@@ -917,7 +927,7 @@ class Uploader {
                     sourceSize: item.sourceSize,
                     storedSize: item.storedSize,
                     mediaType: item.mediaType,
-                    executable: false,
+                    executable: item.executable === true,
                 })),
             }),
         }));
@@ -1719,6 +1729,7 @@ class Uploader {
                     sourceSize: Number(row.sourceSize ?? 0),
                     storedSize: Number(row.storedSize ?? 0),
                     mediaType: String(row.mediaType ?? "application/octet-stream"),
+                    executable: row.executable === true,
                 });
             }
         }
@@ -2629,3 +2640,23 @@ class Uploader {
     }
 }
 exports.Uploader = Uploader;
+/**
+ * Whether a file being sent is marked to run.
+ *
+ * The caller's word first, then the file's own mode. Windows has no execute
+ * bit to read, so there a file keeps whatever the previous version said,
+ * rather than every save from Windows quietly clearing it.
+ */
+async function executableFor(request, relative, before) {
+    const told = request.executable?.get(relative);
+    if (told !== undefined)
+        return told;
+    if (process.platform === "win32")
+        return before;
+    try {
+        return ((await (0, promises_1.stat)(node_path_1.default.join(request.localPath, relative))).mode & 0o111) !== 0;
+    }
+    catch {
+        return before;
+    }
+}

package/dist/cbx/src/local/remote.js

@@ -226,6 +226,8 @@ async function push(repository, options) {
                       the wrong ones. The git push sends this for the same reason.
                     */
                     allowIgnored: true,
+                    /* The save's own record of what runs; on Windows the scratch tree cannot say. */
+                    executable: new Map([...after].map(([file, entry]) => [file, entry.executable])),
                     ...(options.allowSecrets ? { allowSecrets: true } : {}),
                     ...(options.acknowledged ? { acknowledged: true } : {}),
                     ...(known ? { known } : {}),
@@ -325,7 +327,11 @@ async function pull(repository, options) {
                     const was = before.get(file.path);
                     const reuse = was?.sha256 === file.sha256 ? was : byDigest.get(file.sha256);
                     if (reuse) {
-                        entries.push({ ...reuse, path: file.path, executable: was?.executable ?? reuse.executable });
+                        entries.push({
+                            ...reuse,
+                            path: file.path,
+                            executable: file.executable ?? was?.executable ?? reuse.executable,
+                        });
                     }
                     else {
                         fetch.push(file);
@@ -347,7 +353,7 @@ async function pull(repository, options) {
                         path: file.path,
                         size: file.sourceSize,
                         sha256: stored.sha256,
-                        executable: before.get(file.path)?.executable ?? false,
+                        executable: file.executable ?? before.get(file.path)?.executable ?? false,
                         chunks: stored.chunks,
                     };
                     entries.push(entry);

package/dist/cli/src/api.js

@@ -58,6 +58,7 @@ exports.addWebhook = addWebhook;
 exports.removeWebhook = removeWebhook;
 exports.collisionCheck = collisionCheck;
 /** The small part of the API the command-line tool needs directly. */
+const network_js_1 = require("./network.js");
 const identify_js_1 = require("../../cbx/src/core/identify.js");
 const config_js_1 = require("./config.js");
 /**
@@ -99,18 +100,36 @@ async function call(route, options = {}) {
     if (!token) {
         throw new Error("Not signed in. Run: cbx sign-in");
     }
-    const response = await fetch(`${(0, config_js_1.apiOrigin)()}${route}`, {
-        method: options.method ?? "GET",
-        headers: {
-            accept: "application/json",
-            authorization: `Bearer ${token}`,
-            "user-agent": "CodeRook-CLI/0.1",
-            ...(0, identify_js_1.clientHeaders)(),
-            ...(options.body ? { "content-type": "application/json" } : {}),
-        },
-        body: options.body ? JSON.stringify(options.body) : undefined,
-        signal: AbortSignal.timeout(REQUEST_DEADLINE_MS),
-    });
+    const method = options.method ?? "GET";
+    /*
+      A read that failed before any answer is asked again, twice, with a pause.
+      Only reads: a write that may have landed is the caller's to retry, with
+      what it knows about idempotency.
+    */
+    let response;
+    for (let attempt = 1;; attempt += 1) {
+        try {
+            response = await fetch(`${(0, config_js_1.apiOrigin)()}${route}`, {
+                method,
+                headers: {
+                    accept: "application/json",
+                    authorization: `Bearer ${token}`,
+                    "user-agent": "CodeRook-CLI/0.1",
+                    ...(0, identify_js_1.clientHeaders)(),
+                    ...(options.body ? { "content-type": "application/json" } : {}),
+                },
+                body: options.body ? JSON.stringify(options.body) : undefined,
+                signal: AbortSignal.timeout(REQUEST_DEADLINE_MS),
+            });
+            break;
+        }
+        catch (error) {
+            if (method !== "GET" || attempt >= 3 || !(0, network_js_1.isNetworkFailure)(error)) {
+                throw new Error((0, network_js_1.describeError)(error), { cause: error });
+            }
+            await (0, network_js_1.pause)(500 * attempt);
+        }
+    }
     const text = await response.text();
     const body = text ? JSON.parse(text) : {};
     if (!response.ok) {
@@ -299,7 +318,16 @@ async function findProject(reference) {
       the authenticated listing knows about private projects the public one
       cannot see.
     */
-    const all = await projects().catch(() => []);
+    /*
+      Only the service saying no becomes "no projects". A network failure or a
+      missing sign-in is said as itself: swallowing it here turned a timeout
+      into "No project matching", which sent somebody looking for a typo.
+    */
+    const all = await projects().catch((error) => {
+        if (error instanceof ServiceError)
+            return [];
+        throw error;
+    });
     const ownersMatch = (project) => project.slug.toLowerCase() === bare || project.name.toLowerCase() === bare;
     if (!owner) {
         const mine = all.find(ownersMatch);

package/dist/cli/src/cli.js

@@ -18,6 +18,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const promises_1 = require("node:readline/promises");
 const node_os_1 = __importDefault(require("node:os"));
 const promises_2 = require("node:fs/promises");
+const node_crypto_1 = require("node:crypto");
 const node_fs_1 = require("node:fs");
 const node_path_1 = __importDefault(require("node:path"));
 const node_process_1 = __importDefault(require("node:process"));
@@ -45,6 +46,7 @@ const faults_js_1 = require("../../cbx/src/core/faults.js");
 const version_commands_js_1 = require("./version_commands.js");
 const identify_js_1 = require("../../cbx/src/core/identify.js");
 const diff_command_js_1 = require("./diff_command.js");
+const network_js_1 = require("./network.js");
 const local_commands_js_1 = require("./local_commands.js");
 const profile_js_1 = require("../../cbx/src/core/profile.js");
 const detect_js_1 = require("../../cbx/src/core/detect.js");
@@ -604,9 +606,51 @@ async function commandImport(parsed) {
     }
     return code;
 }
+/** A file's SHA-256, streamed; null when it cannot be read. */
+async function digestOfFile(full) {
+    try {
+        const hash = (0, node_crypto_1.createHash)("sha256");
+        for await (const block of (0, node_fs_1.createReadStream)(full))
+            hash.update(block);
+        return hash.digest("hex");
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Say so when files deleted here are still in the saved version.
+ *
+ * A plain save adds and updates and never removes, so a deleted or moved file
+ * lives on in every save after it until somebody passes --sync. `status`
+ * already said this; `submit` did not, and from Linux a project turned out to
+ * carry a stale copy of a whole app at its root for weeks. Counted from the
+ * folder's record of what it holds, so it costs a stat per recorded file.
+ */
+function noteKeptDeletions(folder, baseline, syncing) {
+    if (syncing || !baseline?.size)
+        return;
+    const gone = [...baseline.keys()].filter((file) => !(0, node_fs_1.existsSync)(node_path_1.default.join(folder, ...file.split("/"))));
+    if (!gone.length)
+        return;
+    console.log(dim(`${gone.length} file${gone.length === 1 ? "" : "s"} deleted here ${gone.length === 1 ? "is" : "are"} still in the saved version` +
+        ` (${gone.slice(0, 3).join(", ")}${gone.length > 3 ? ", …" : ""}). A save adds and updates;` +
+        ` run cbx submit --sync to remove ${gone.length === 1 ? "it" : "them"}.`));
+}
 async function commandSubmit(parsed) {
     const folder = folderFor(parsed);
     const message = flagText(parsed, "m", "message") ?? "";
+    /*
+      Checked before anything is scanned or planned. The service's own refusal
+      arrived after the upload plan had been printed, as a schema error about
+      "<=240 characters", which reads like a fault rather than a limit.
+    */
+    if (message.trim().length > 240) {
+        console.error(red(`The message is ${message.trim().length} characters; the limit is 240.`));
+        console.error(dim("Put the detail in release notes or a NOTES file, and keep the message to a line."));
+        return 1;
+    }
+    const dryRun = hasFlag(parsed, "dry-run", "n");
     const { link, baseline, behind, member } = await reconcile(folder);
     /*
       Somebody else's project, cloned from its public page. Reading and
@@ -632,7 +676,12 @@ async function commandSubmit(parsed) {
       Only on a project's first save. After that an absent LICENSE is somebody's
       decision and putting one back would be arguing with them.
     */
-    const added = link
+    /*
+      A dry run changes nothing, and that includes writing a LICENSE: it says
+      what would be added instead.
+    */
+    const wouldLicence = dryRun && !link && !hasFlag(parsed, "no-licence") && !(0, node_fs_1.existsSync)(node_path_1.default.join(folder, "LICENSE"));
+    const added = link || dryRun
         ? null
         : await (0, licence_commands_js_1.licenceNewProject)(folder, 
         /*
@@ -836,6 +885,10 @@ Pass ${accent("--allow-secrets")} if these are not real keys.`);
         }
         console.log(dim("Sending them anyway, because --allow-secrets was given."));
     }
+    if (wouldLicence) {
+        console.log(`${accent("Would add an MIT licence")} on a real save, so other people may use this.` +
+            dim(" Pass --no-licence to leave it out."));
+    }
     if (added) {
         console.log(`${accent("Added an MIT licence")}, so other people may use this.`);
         console.log(dim(`  Change it with `) +
@@ -846,7 +899,7 @@ Pass ${accent("--allow-secrets")} if these are not real keys.`);
         console.log("");
     }
     const line = progressLine();
-    const uploader = new upload_js_1.Uploader(config_js_1.credentials);
+    let uploader = new upload_js_1.Uploader(config_js_1.credentials);
     /*
       Built by the shared description, so this and the git remote helper cannot
       drift. They already had: the helper listed deletions in `deletions` alone
@@ -948,63 +1001,99 @@ Pass ${accent("--allow-secrets")} if these are not real keys.`);
         }
     }
     let result;
-    try {
-        const plan = await uploader.plan(uploadRequest, (progress) => {
-            line(`  ${track(progress.percent)} ${String(progress.percent).padStart(3)}%  ` +
-                `${"plan".padEnd(7)} ${progress.files}/${progress.totalFiles}  ` +
-                dim(progress.path.slice(-40)));
-        });
-        done(line);
-        console.log(`${accent("Upload plan")}  ${bytes(plan.sourceBytes)} selected → ` +
-            `${bytes(plan.compactedBytes)} compacted; ${bytes(plan.chargeableBytes)} new storage.`);
-        console.log(plan.allowance.exempt
-            ? dim("Annual plan: the monthly staged upload allowance does not apply.")
-            : dim(`Monthly stage ${plan.allowance.stage}: ${plan.allowance.unlockedPercent}% unlocked, ` +
-                `${bytes(plan.allowance.remainingBytes)} remains after this reservation.`));
-        if (hasFlag(parsed, "dry-run", "n")) {
-            await uploader.cancelPlan(plan, true);
-            console.log(`${files.length} file${files.length === 1 ? "" : "s"} would be sent or reused:`);
-            for (const file of files)
-                console.log(`  ${file.path}`);
-            console.log("Nothing was uploaded and no Version was created.");
-            return 0;
-        }
-        result = await uploader.execute(uploadRequest, plan, (progress) => {
-            line(`  ${track(progress.percent)} ${String(progress.percent).padStart(3)}%  ` +
-                `${progress.stage.padEnd(7)} ${progress.files}/${progress.totalFiles}  ` +
-                dim(progress.path.slice(-40)));
-        });
-    }
-    catch (error) {
-        done(line);
-        /*
-          Classified by the shared description rather than by a private regular
-          expression, so a push and a submit disagree about nothing — including
-          what counts as "the connection failed" and what that means for whether
-          the work was saved.
-        */
-        const failure = (0, publish_js_1.classifyPublishFailure)(error);
-        const text = error instanceof Error ? error.message : String(error);
-        if (failure?.kind === "interrupted") {
-            console.error(red(`
-The connection failed: ${text}`));
-            console.error(`Your work may already have been saved. Run the same command again —` +
-                ` it will not create a second version.`);
-            return 1;
+    /*
+      How long to wait before picking a dropped upload up again by itself.
+  
+      Each request is already retried for a few seconds, but a Wi-Fi drop or a
+      router reconnecting outlasts that, and the upload ended with "run the same
+      command again" for somebody to notice and act on. Running it again was
+      always safe and cheap (pieces already stored are recognised and skipped,
+      and the save itself is named so it can never be made twice), so the
+      command now does it itself, a few times, before giving up.
+    */
+    const resumeAfter = [10, 30, 60];
+    for (let resumed = 0;; resumed += 1) {
+        try {
+            const plan = await uploader.plan(uploadRequest, (progress) => {
+                line(`  ${track(progress.percent)} ${String(progress.percent).padStart(3)}%  ` +
+                    `${"plan".padEnd(7)} ${progress.files}/${progress.totalFiles}  ` +
+                    dim(progress.path.slice(-40)));
+            });
+            done(line);
+            console.log(`${accent("Upload plan")}  ${bytes(plan.sourceBytes)} selected → ` +
+                `${bytes(plan.compactedBytes)} compacted; ${bytes(plan.chargeableBytes)} new storage.`);
+            console.log(plan.allowance.exempt
+                ? dim("Annual plan: the monthly staged upload allowance does not apply.")
+                : dim(`Monthly stage ${plan.allowance.stage}: ${plan.allowance.unlockedPercent}% unlocked, ` +
+                    `${bytes(plan.allowance.remainingBytes)} remains after this reservation.`));
+            if (dryRun) {
+                await uploader.cancelPlan(plan, true);
+                const going = files.filter((file) => !file.deleted);
+                const removing = files.filter((file) => file.deleted);
+                console.log(`${going.length} file${going.length === 1 ? "" : "s"} would be sent or reused:`);
+                for (const file of going)
+                    console.log(`  ${file.path}`);
+                if (removing.length) {
+                    console.log(`${removing.length} file${removing.length === 1 ? "" : "s"} would be removed from the save:`);
+                    for (const file of removing)
+                        console.log(`  ${red("deleted")} ${file.path}`);
+                }
+                noteKeptDeletions(folder, baseline, hasFlag(parsed, "sync"));
+                console.log("Nothing was uploaded and no Version was created.");
+                return 0;
+            }
+            result = await uploader.execute(uploadRequest, plan, (progress) => {
+                line(`  ${track(progress.percent)} ${String(progress.percent).padStart(3)}%  ` +
+                    `${progress.stage.padEnd(7)} ${progress.files}/${progress.totalFiles}  ` +
+                    dim(progress.path.slice(-40)));
+            });
+            break;
         }
-        if (failure?.kind === "conflict") {
+        catch (error) {
+            done(line);
             /*
-              Somebody else saved to this project first. Everything that did not
-              overlap has already been combined by the service; what is left is a
-              genuine decision, so the answer is to bring their work down and look
-              at it rather than to try again harder.
+              Classified by the shared description rather than by a private regular
+              expression, so a push and a submit disagree about nothing — including
+              what counts as "the connection failed" and what that means for whether
+              the work was saved.
             */
-            console.error(red(error instanceof Error ? error.message : String(error)));
-            console.error(`\nRun ${accent("cbx get")} to bring the latest version down, then` +
-                ` submit again. Nothing was changed on your account.`);
-            return 1;
+            const failure = (0, publish_js_1.classifyPublishFailure)(error);
+            const text = (0, network_js_1.describeError)(error);
+            if (failure?.kind === "interrupted" && !dryRun && resumed < resumeAfter.length) {
+                const wait = resumeAfter[resumed];
+                console.error(dim(`The connection dropped (${text})`));
+                console.error(dim(`Picking the upload up again in ${wait}s (try ${resumed + 2} of ${resumeAfter.length + 1}).` +
+                    ` Pieces already sent are kept; only the rest goes.`));
+                /*
+                  The failed attempt's other lanes are still retrying; stopped first, so
+                  they do not carry on sending beside the attempt that replaces them.
+                */
+                uploader.cancel();
+                await (0, network_js_1.pause)(wait * 1000);
+                uploader = new upload_js_1.Uploader(config_js_1.credentials);
+                continue;
+            }
+            if (failure?.kind === "interrupted") {
+                console.error(red(`
+The connection failed: ${text}`));
+                console.error(`Your work may already have been saved. Run the same command again —` +
+                    ` it will not create a second version.`);
+                return 1;
+            }
+            if (failure?.kind === "conflict") {
+                /*
+                  Somebody else saved to this project first. Everything that did not
+                  overlap has already been combined by the service; what is left is a
+                  genuine decision, so the answer is to bring their work down and look
+                  at it rather than to try again harder.
+                */
+                console.error(red(error instanceof Error ? error.message : String(error)));
+                console.error(`\nRun ${accent("cbx get")} to bring the latest version down, then` +
+                    ` submit again. Nothing was changed on your account.`);
+                return 1;
+            }
+            throw error;
         }
-        throw error;
     }
     done(line);
     if (result.mergeTrack) {
@@ -1105,6 +1194,7 @@ The connection failed: ${text}`));
           command does not do.
         */
         ` · the save holds ${bytes(result.sourceBytes)}`);
+    noteKeptDeletions(folder, baseline, hasFlag(parsed, "sync"));
     /*
       Where the time went, when asked for.
   
@@ -1236,9 +1326,23 @@ Save them with ${accent("cbx submit")}, or finish the fetch and ` +
               and stopping for those would make the warning something people learn
               to click past.
             */
-            const atRisk = edited.filter((file) => !file.deleted &&
-                incoming.has(file.path) &&
-                incoming.get(file.path) !== link.local[file.path]);
+            const atRisk = [];
+            for (const file of edited) {
+                if (file.deleted || !incoming.has(file.path))
+                    continue;
+                if (incoming.get(file.path) === link.local[file.path])
+                    continue;
+                /*
+                  Already exactly what is arriving: nothing would be lost by writing
+                  it. This is what the same folder looks like after being saved from
+                  another machine or another operating system, and refusing it left
+                  a folder that could neither fetch nor save without a merge.
+                */
+                const here = await digestOfFile(node_path_1.default.join(folder, ...file.path.split("/")));
+                if (here === incoming.get(file.path))
+                    continue;
+                atRisk.push(file);
+            }
             if (atRisk.length) {
                 console.error(red(`${atRisk.length} file${atRisk.length === 1 ? "" : "s"} here ` +
                     `${atRisk.length === 1 ? "has" : "have"} changes that fetching would overwrite:`));
@@ -1382,6 +1486,15 @@ trackName) {
     // dropped is removed while everything untracked is left alone.
     held, mode);
     done(line);
+    /*
+      Said, not hidden. The files are right, but the service sent them still
+      compressed, which means its record of how they are stored is wrong.
+    */
+    if (downloader.recoveredFromGzip.length) {
+        console.log(dim(`${downloader.recoveredFromGzip.length} file${downloader.recoveredFromGzip.length === 1 ? "" : "s"} ` +
+            `arrived still compressed and were unpacked here; the copies are exact. ` +
+            `Tell security@coderook.com if this keeps happening.`));
+    }
     // Fetching is how a folder catches up, so this is what moves its base.
     await (0, config_js_1.writeLink)(destination, {
         repositoryId,
@@ -3119,9 +3232,10 @@ async function main(argv) {
 function leave(code) {
     node_process_1.default.exitCode = code;
 }
+(0, network_js_1.tuneNetwork)();
 main(node_process_1.default.argv.slice(2))
     .then(leave)
     .catch((error) => {
-    console.error(red(error instanceof Error ? error.message : String(error)));
+    console.error(red((0, network_js_1.describeError)(error)));
     leave(1);
 });

package/dist/cli/src/config.js

@@ -319,18 +319,66 @@ async function lookUp(localPath) {
         if (!stored)
             continue;
         if ("forgotten" in stored)
-            return null;
+            return "forgotten";
         return unpack(stored);
     }
     return null;
 }
+/*
+  A copy of the link kept in the folder itself, beside the offline outbox.
+
+  The machine's own record is keyed by the folder's path, so the same folder
+  seen from another operating system (a drive letter from Windows, a mount
+  point from Linux, on the same disk) or from another machine was a stranger,
+  and every project had to be cloned again into a new folder. `.coderook` is
+  never scanned or uploaded, and the copy holds no token: only which project
+  and version the folder stands on, as `.git` records its remote.
+*/
+const folderLinkFile = (localPath) => node_path_1.default.join(node_path_1.default.resolve(localPath), ".coderook", "link.json");
+async function readFolderLink(localPath) {
+    try {
+        const raw = JSON.parse(await (0, promises_1.readFile)(folderLinkFile(localPath), "utf8"));
+        if (typeof raw.repositoryId !== "string" || typeof raw.slug !== "string")
+            return null;
+        return {
+            ...raw,
+            manifest: raw.manifest ?? {},
+            sequence: Number(raw.sequence ?? 0),
+        };
+    }
+    catch {
+        return null;
+    }
+}
+async function writeFolderLink(localPath, link) {
+    try {
+        const directory = node_path_1.default.dirname(folderLinkFile(localPath));
+        await (0, promises_1.mkdir)(directory, { recursive: true });
+        /* Git leaves it alone too, without anybody editing their .gitignore. */
+        await (0, promises_1.writeFile)(node_path_1.default.join(directory, ".gitignore"), "*\n").catch(() => undefined);
+        await (0, promises_1.writeFile)(folderLinkFile(localPath), JSON.stringify(link));
+    }
+    catch {
+        /* A folder that cannot hold the copy still has the machine's record. */
+    }
+}
 async function readLink(localPath) {
-    let link = await lookUp(localPath);
-    if (!link &&
+    let found = await lookUp(localPath);
+    if (!found &&
         ((await exists(legacyLinksFile())) ||
             (await exists(`${legacyLinksFile()}.migrating`)))) {
         await migrateLegacyLinks();
-        link = await lookUp(localPath);
+        found = await lookUp(localPath);
+    }
+    /* Unlinked on this machine on purpose: the folder's copy does not overrule that. */
+    if (found === "forgotten")
+        return null;
+    let link = found;
+    if (!link) {
+        link = await readFolderLink(localPath);
+        /* Adopted, so this machine knows the folder from now on. */
+        if (link)
+            await writeLink(localPath, link);
     }
     if (!link)
         return null;
@@ -353,6 +401,7 @@ async function forgetLink(localPath) {
         const forgotten = { key, forgotten: true };
         await writePrivate(storedFileFor(key), JSON.stringify(forgotten));
     }
+    await (0, promises_1.rm)(folderLinkFile(localPath), { force: true });
     return true;
 }
 async function writeLink(localPath, link) {
@@ -363,6 +412,10 @@ async function writeLink(localPath, link) {
         ...(baseVersionId ? { baseVersionId, versionId: baseVersionId } : {}),
     });
     await writePrivate(storedFileFor(key), JSON.stringify(stored));
+    await writeFolderLink(localPath, {
+        ...link,
+        ...(baseVersionId ? { baseVersionId, versionId: baseVersionId } : {}),
+    });
     // A folder recorded under the old key moves to the new one rather than
     // being left behind as a second connection to the same place.
     const legacy = legacyKeyFor(localPath);

package/dist/cli/src/git_remote.js

@@ -88,9 +88,9 @@ exports.main = main;
  *   is nothing to rewind to. Both are refused rather than silently ignored.
  * - **Submodules.** A gitlink is a pointer into another repository and there
  *   are no bytes to publish. Skipped on push, and said out loud.
- * - **File modes.** Everything is imported as `100644`. CodeRook records an
- *   executable bit but git's mode is not round-tripped yet, so a script
- *   cloned back needs `chmod +x`.
+ * - **File modes.** The executable bit travels both ways: a pushed `100755`
+ *   is recorded as executable, and an executable file is fetched as `100755`.
+ *   Versions saved before the bit was recorded come back `100644`.
  *
  * ## What a round trip does and does not preserve
  *
@@ -284,6 +284,7 @@ async function applyCommit(catFile, scratch, fromCommit, toCommit) {
     const written = [];
     const deleted = [];
     const skipped = [];
+    const executable = new Map();
     for (let index = 0; index + 1 < fields.length; index += 2) {
         const status = fields[index];
         const filePath = fields[index + 1];
@@ -309,8 +310,9 @@ async function applyCommit(catFile, scratch, fromCommit, toCommit) {
         await (0, promises_1.mkdir)(node_path_1.default.dirname(target), { recursive: true });
         await (0, promises_1.writeFile)(target, bytes);
         written.push(filePath);
+        executable.set(filePath, mode === "100755");
     }
-    return { written, deleted, skipped };
+    return { written, deleted, skipped, executable };
 }
 /*
   The service's answer when a line is already there.
@@ -838,7 +840,7 @@ depth = null) {
                 */
                 if (file.path.split("/").some(safe_path_js_1.isGitDirectoryName))
                     continue;
-                send(`M 100644 :${blobMark.get(file.sha256)} ${(0, git_history_js_1.quotePath)(file.path)}`);
+                send(`M ${file.executable ? "100755" : "100644"} :${blobMark.get(file.sha256)} ${(0, git_history_js_1.quotePath)(file.path)}`);
             }
             send("");
             done += 1;
@@ -1305,6 +1307,7 @@ async function doPush(requests, url) {
                     baseVersionId,
                     track: branch,
                     allowIgnored: true,
+                    executable: changes.executable,
                     ...(Object.keys(manifest).length ? { known: local } : {}),
                 });
                 let result;

package/dist/cli/src/licence_commands.js

@@ -111,12 +111,28 @@ async function commandLicence(parsed) {
     */
     let holder = flagValue(parsed, "holder") ?? "";
     if (licence.personalised && !holder) {
+        /*
+          Why the name could not be had decides what to say. This used to answer
+          every failure with "sign in", including a network timeout for somebody
+          who was signed in, and sent them to fix the wrong thing.
+        */
+        let failure = null;
         holder = await (0, api_js_1.whoami)()
             .then((account) => account.displayName || account.username || "")
-            .catch(() => "");
+            .catch((error) => {
+            failure = error;
+            return "";
+        });
         if (!holder) {
+            const reason = failure instanceof Error ? failure.message : "";
             console.error(red("Could not work out whose name goes on the licence."));
-            console.error(`Sign in, or pass ${accent('--holder "Your Name"')} to say directly.`);
+            if (/sign-in|not signed in|not accepted/i.test(reason) || !failure) {
+                console.error(`Sign in, or pass ${accent('--holder "Your Name"')} to say directly.`);
+            }
+            else {
+                console.error(dim(reason));
+                console.error(`Try again, or pass ${accent('--holder "Your Name"')} to say directly.`);
+            }
             return 1;
         }
     }

package/dist/cli/src/network.js

@@ -0,0 +1,77 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.tuneNetwork = tuneNetwork;
+exports.isNetworkFailure = isNetworkFailure;
+exports.describeError = describeError;
+exports.pause = pause;
+/**
+ * Reaching the service on networks that half-support IPv6.
+ *
+ * Found from Linux: a router hands out IPv6 addresses but has no IPv6 route.
+ * Node tries both families at once and gives each address 250 ms. The IPv6
+ * attempt fails at once, and an IPv4 handshake that occasionally takes longer
+ * than 250 ms is abandoned too, so a perfectly healthy connection came back as
+ * the two words "fetch failed". curl and browsers never showed it.
+ */
+const node_dns_1 = __importDefault(require("node:dns"));
+const node_net_1 = __importDefault(require("node:net"));
+/** Called once, before any request. Explicit settings in NODE_OPTIONS win. */
+function tuneNetwork() {
+    const options = process.env.NODE_OPTIONS ?? "";
+    if (!options.includes("autoselection-attempt-timeout")) {
+        try {
+            node_net_1.default.setDefaultAutoSelectFamilyAttemptTimeout(1_000);
+        }
+        catch {
+            /* Older Node: nothing to tune. */
+        }
+    }
+    if (!options.includes("dns-result-order")) {
+        try {
+            node_dns_1.default.setDefaultResultOrder("ipv4first");
+        }
+        catch {
+            /* Older Node: nothing to tune. */
+        }
+    }
+}
+/** Whether a failure happened before any answer came back. */
+function isNetworkFailure(error) {
+    if (!(error instanceof Error))
+        return false;
+    if (error.name === "TimeoutError" || error.name === "AbortError")
+        return true;
+    return error.message === "fetch failed" || Boolean(error.cause);
+}
+/**
+ * The real reason, instead of "fetch failed".
+ *
+ * Node puts what went wrong in `cause` (and, for a failed happy-eyeballs
+ * connection, in `cause.errors`, one per address tried). Naming the code and
+ * the address is what lets somebody tell a dead network from a slow one.
+ */
+function describeError(error) {
+    if (!(error instanceof Error))
+        return String(error);
+    if (error.name === "TimeoutError") {
+        return "CodeRook did not answer in time. Check the connection, then try again.";
+    }
+    const cause = error.cause;
+    if (error.message === "fetch failed" && cause) {
+        const attempts = cause.errors?.length ? cause.errors : [cause];
+        const named = attempts
+            .map((one) => [one.code, one.address].filter(Boolean).join(" "))
+            .filter(Boolean);
+        if (named.length) {
+            return `Could not reach CodeRook (${[...new Set(named)].join(", ")}). Check the connection, then try again.`;
+        }
+    }
+    return error.message;
+}
+/** Wait, for a retry. */
+function pause(milliseconds) {
+    return new Promise((resolve) => setTimeout(resolve, milliseconds));
+}

package/dist/cli/src/publish.js

@@ -19,6 +19,7 @@ function uploadRequestFor(input) {
         ...(input.allowSecrets ? { allowSecrets: true } : {}),
         ...(input.acknowledged ? { acknowledged: true } : {}),
         ...(input.acknowledgedNoLicence ? { acknowledgedNoLicence: true } : {}),
+        ...(input.executable ? { executable: input.executable } : {}),
         ...(input.baseVersionId
             ? { expectedHeadVersionId: input.baseVersionId }
             : {}),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@coderook/cli",
-  "version": "0.32.1",
+  "version": "0.33.1",
   "description": "The command line for CodeRook (coderook.com): version control and project hosting for projects of any size. Every save is a compressed snapshot, private or public, never used to train AI.",
   "license": "Apache-2.0",
   "homepage": "https://coderook.com",