@rotifer/playground 0.8.5 → 0.9.0

package/dist/commands/publish.js

@@ -47,6 +47,9 @@ const domain_suggest_js_1 = require("../utils/domain-suggest.js");
 const validate_gene_name_js_1 = require("../utils/validate-gene-name.js");
 const content_hash_js_1 = require("../utils/content-hash.js");
 const pre_publish_check_js_1 = require("../publish/pre-publish-check.js");
+const detect_source_language_js_1 = require("../utils/detect-source-language.js");
+const badge_js_1 = require("../cloud/badge.js");
+const VG_SCANNER_VERSION = "0.8.0";
 function formatCheckIcon(status) {
     if (status === "pass")
         return palette_js_1.c.success(palette_js_1.icon.success);
@@ -62,8 +65,10 @@ async function publishSingleGene(geneName, geneDir, creds, options, isQuiet = fa
         }
         return { name: geneName, status: "skipped", error: "no phenotype.json" };
     }
+    let scanResult = null;
     if (!options.skipSecurity) {
         const checkResult = (0, pre_publish_check_js_1.runPrePublishChecks)(geneDir, geneName);
+        scanResult = checkResult.scanResult;
         if (!isQuiet) {
             for (const check of checkResult.checks) {
                 console.log(`  ${formatCheckIcon(check.status)} ${check.name}: ${check.message}`);
@@ -91,6 +96,9 @@ async function publishSingleGene(geneName, geneDir, creds, options, isQuiet = fa
         }
     }
     const fidelity = phenotype.fidelity || "Wrapped";
+    if (!phenotype.synthesisMethod) {
+        phenotype.synthesisMethod = "MANUAL";
+    }
     const irWasmPath = (0, node_path_1.join)(geneDir, "gene.ir.wasm");
     const wasmBytes = (0, node_fs_1.existsSync)(irWasmPath)
         ? (0, node_fs_1.readFileSync)(irWasmPath)
@@ -125,6 +133,29 @@ async function publishSingleGene(geneName, geneDir, creds, options, isQuiet = fa
             error: `Invalid domain format '${domain}'. Use lowercase letters, numbers, and dots (e.g. 'media.video').`,
         };
     }
+    const explicitLang = options.lang?.toLowerCase();
+    if (explicitLang && !(0, detect_source_language_js_1.isValidSourceLanguage)(explicitLang)) {
+        return {
+            name: geneName,
+            status: "failed",
+            error: `Invalid --lang value '${options.lang}'. Allowed: typescript|rust|assemblyscript|go|c|external|unknown`,
+        };
+    }
+    const detectedLang = (0, detect_source_language_js_1.detectSourceLanguage)(geneDir);
+    const sourceLanguage = explicitLang ??
+        (typeof phenotype.sourceLanguage === "string" &&
+            (0, detect_source_language_js_1.isValidSourceLanguage)(phenotype.sourceLanguage)
+            ? phenotype.sourceLanguage
+            : detectedLang);
+    phenotype.sourceLanguage = sourceLanguage;
+    if (!isQuiet) {
+        const origin = explicitLang
+            ? "explicit --lang"
+            : phenotype.sourceLanguage === detectedLang
+                ? "auto-detected"
+                : "from phenotype.json";
+        display.info(`Source language: ${sourceLanguage} (${origin})`);
+    }
     const description = options.description ||
         phenotype.description ||
         `${geneName} gene (${domain})`;
@@ -160,6 +191,7 @@ async function publishSingleGene(geneName, geneDir, creds, options, isQuiet = fa
             published_at: new Date().toISOString(),
         }, null, 2) + "\n");
         const status = result.isUpdate ? "updated" : "created";
+        await tryUploadVgBadge(result.id, scanResult, options, isQuiet);
         if (!options.skipArena && !isQuiet) {
             display.info(`Auto Arena submission skipped for '${geneName}' — verified runtime metrics are required. ` +
                 `Run 'rotifer arena submit ${geneName} --cloud' after evaluation.`);
@@ -170,6 +202,44 @@ async function publishSingleGene(geneName, geneDir, creds, options, isQuiet = fa
         return { name: geneName, status: "failed", error: err.message };
     }
 }
+/**
+ * Upload V(g) safety badge after successful publish (v0.9 §3.8 Phase 1).
+ *
+ * Behavior matrix (see `decideBadgeAction` in src/cloud/badge.ts).
+ * Failures are non-blocking: badge is observability, not protocol.
+ */
+async function tryUploadVgBadge(geneUuid, scanResult, options, isQuiet) {
+    const token = process.env.ROTIFER_BADGE_TOKEN;
+    if (!token) {
+        if (!isQuiet) {
+            display.hint("Skipping V(g) badge upload (ROTIFER_BADGE_TOKEN not set)");
+        }
+        return;
+    }
+    const action = (0, badge_js_1.decideBadgeAction)({
+        skipVg: options.skipVg,
+        skipSecurity: options.skipSecurity,
+        hasScanResult: scanResult !== null,
+    });
+    if (action.kind === "skip") {
+        if (!isQuiet) {
+            display.hint(`Skipping V(g) badge upload (${action.reason})`);
+        }
+        return;
+    }
+    const payload = action.mode === "skipped" ? null : scanResult;
+    const r = await (0, badge_js_1.uploadSafetyBadge)(geneUuid, payload, VG_SCANNER_VERSION, action.mode, token);
+    if (!isQuiet) {
+        if (r.ok) {
+            const detail = action.mode === "skipped" ? "skipped" : `grade ${payload?.grade ?? "?"}`;
+            display.success(`V(g) badge uploaded (${detail})`);
+        }
+        else {
+            const detail = r.status ? `${r.status} ${r.error ?? ""}` : (r.error ?? "");
+            display.warn(`V(g) badge upload failed (non-blocking): ${detail}`);
+        }
+    }
+}
 exports.publishCommand = new commander_1.Command("publish")
     .description("Publish gene(s) to Rotifer Cloud")
     .argument("[gene-name]", "gene name to publish (omit when using --all)")
@@ -177,7 +247,9 @@ exports.publishCommand = new commander_1.Command("publish")
     .option("--changelog <text>", "changelog entry for this version (max 500 chars)")
     .option("--skip-arena", "skip automatic Arena submission and reputation computation")
     .option("--skip-security", "skip pre-publish security checks (dangerous API / IR / secrets scan)")
+    .option("--skip-vg", "skip V(g) safety scan and upload 'skipped' badge placeholder (badge displays 'skipped')")
     .option("--all", "publish all valid genes in the genes directory")
+    .option("--lang <lang>", "explicitly declare source language (typescript|rust|assemblyscript|go|c|external)")
     .action(async (geneName, options) => {
     if (!geneName && !options.all) {
         display.error("Provide a gene name or use --all to publish all genes.");

package/dist/commands/publish.js.map

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package/dist/commands/reputation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reputation.d.ts","sourceRoot":"","sources":["../../src/commands/reputation.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAMpC,eAAO,MAAM,iBAAiB,SAgC3B,CAAC"}
+{"version":3,"file":"reputation.d.ts","sourceRoot":"","sources":["../../src/commands/reputation.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAapC,eAAO,MAAM,iBAAiB,SAsC3B,CAAC"}

package/dist/commands/reputation.js

@@ -39,13 +39,14 @@ const display = __importStar(require("../utils/display.js"));
 const palette_js_1 = require("../utils/palette.js");
 const client_js_1 = require("../cloud/client.js");
 const auth_js_1 = require("../cloud/auth.js");
+const gene_ref_js_1 = require("../cloud/gene-ref.js");
 exports.reputationCommand = new commander_1.Command("reputation")
     .description("View gene and creator reputation scores")
-    .argument("[gene-ref]", "gene UUID, name, or content hash")
+    .argument("[ref]", "gene ref (UUID, name, content hash, @owner/name) or @username")
     .option("--mine", "show your creator reputation", false)
     .option("--leaderboard", "show creator leaderboard", false)
     .option("--top <n>", "number of entries in leaderboard", "10")
-    .action(async (geneRef, options) => {
+    .action(async (ref, options) => {
     if (options.leaderboard) {
         await showLeaderboard(parseInt(options.top, 10));
         return;
@@ -54,12 +55,18 @@ exports.reputationCommand = new commander_1.Command("reputation")
         await showMyReputation();
         return;
     }
-    if (geneRef) {
-        await showGeneReputation(geneRef);
+    if (ref) {
+        const userRef = (0, gene_ref_js_1.parseUserRef)(ref);
+        if (userRef) {
+            await showUserReputation(userRef.username);
+            return;
+        }
+        await showGeneReputation(ref);
         return;
     }
-    display.error("Specify a gene reference, --mine, or --leaderboard");
-    display.hint("Usage: rotifer reputation <gene-ref>");
+    display.error("Specify a gene reference, @username, --mine, or --leaderboard");
+    display.hint("Usage: rotifer reputation <gene-ref>          # by UUID, name, or @owner/name");
+    display.hint("       rotifer reputation @username            # creator reputation");
     display.hint("       rotifer reputation --mine");
     display.hint("       rotifer reputation --leaderboard");
     process.exit(1);
@@ -67,7 +74,11 @@ exports.reputationCommand = new commander_1.Command("reputation")
 async function showGeneReputation(geneRef) {
     const s = display.spinner("Fetching gene reputation...");
     try {
-        const rep = await (0, client_js_1.getGeneReputation)(geneRef);
+        // Resolve any user-facing ref (UUID / contentHash / @owner/name / plain
+        // name) into the gene UUID first; getGeneReputation expects a UUID and
+        // PostgreSQL throws a UUID-parse error otherwise (Issue #50 Bug 3).
+        const gene = await (0, client_js_1.getGene)(geneRef);
+        const rep = await (0, client_js_1.getGeneReputation)(gene.id);
         s.stop();
         display.renderResult(rep, (data) => {
             display.header("Gene Reputation");
@@ -101,12 +112,42 @@ async function showMyReputation() {
         process.exit(1);
         return;
     }
+    await renderCreatorReputation(creds.user.username, creds.user.id, {
+        header: "My Creator Reputation",
+    });
+}
+async function showUserReputation(username) {
+    const s = display.spinner(`Looking up @${username}...`);
+    let profile;
+    try {
+        profile = await (0, client_js_1.getProfileByUsername)(username);
+    }
+    catch (err) {
+        s.stop();
+        const msg = err instanceof Error ? err.message : "Failed to look up user";
+        display.error(msg);
+        display.hint("Check your network connection and try again.");
+        process.exit(1);
+        return;
+    }
+    s.stop();
+    if (!profile) {
+        display.error(`Creator @${username} not found in Rotifer Cloud.`);
+        display.hint("Check the @username spelling, or run 'rotifer reputation --leaderboard' to discover creators.");
+        process.exit(1);
+        return;
+    }
+    await renderCreatorReputation(profile.username, profile.id, {
+        header: `Creator Reputation: @${profile.username}`,
+    });
+}
+async function renderCreatorReputation(username, userId, opts) {
     const s = display.spinner("Fetching creator reputation...");
     try {
-        const rep = await (0, client_js_1.getDeveloperReputation)(creds.user.id);
+        const rep = await (0, client_js_1.getDeveloperReputation)(userId);
         s.stop();
-        display.renderResult({ username: creds.user.username, ...rep }, (data) => {
-            display.header("My Creator Reputation");
+        display.renderResult({ username, ...rep }, (data) => {
+            display.header(opts.header);
             console.log();
             display.kv("Creator", `@${data.username}`);
             display.kv("Overall Score", (0, palette_js_1.scoreColor)(data.score));

package/dist/commands/reputation.js.map

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package/dist/commands/run.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAOpC,eAAO,MAAM,UAAU,SA+HpB,CAAC"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC,eAAO,MAAM,UAAU,SA+IpB,CAAC"}

package/dist/commands/run.js

@@ -39,6 +39,7 @@ const node_fs_1 = require("node:fs");
 const node_path_1 = require("node:path");
 const display = __importStar(require("../utils/display.js"));
 const config_js_1 = require("../utils/config.js");
+const sandbox_defaults_js_1 = require("../utils/sandbox-defaults.js");
 const validate_gene_name_js_1 = require("../utils/validate-gene-name.js");
 exports.runCommand = new commander_1.Command("run")
     .description("Execute a single gene directly")
@@ -55,7 +56,7 @@ exports.runCommand = new commander_1.Command("run")
         root = (0, config_js_1.getProjectRoot)();
     }
     catch {
-        display.error("Not in a Rotifer project. Run 'rotifer init' first.");
+        display.error("Not in a Rotifer Agent workspace. Run 'rotifer init' first.");
         process.exit(1);
         return;
     }
@@ -87,6 +88,7 @@ exports.runCommand = new commander_1.Command("run")
         process.exit(1);
         return;
     }
+    const isSandboxEnabled = !process.argv.includes("--no-sandbox");
     if (options.verbose) {
         display.keyValue("Gene", geneName);
         display.keyValue("Domain", phenotype.domain || "unknown");
@@ -96,15 +98,22 @@ exports.runCommand = new commander_1.Command("run")
     }
     const wasmPath = (0, node_path_1.join)(geneDir, "gene.ir.wasm");
     const sourcePath = (0, node_path_1.join)(geneDir, "index.ts");
-    if ((0, node_fs_1.existsSync)(wasmPath) && options.sandbox) {
+    if ((0, node_fs_1.existsSync)(wasmPath) && isSandboxEnabled) {
+        // #58: warn when the source was edited after the last compile — the
+        // sandbox would otherwise silently execute stale WASM.
+        const { isWasmStale } = await import("../utils/javy-compiler.js");
+        if (isWasmStale(wasmPath, sourcePath)) {
+            display.warn(`gene.ir.wasm is older than index.ts — running stale WASM. Re-run \`rotifer compile ${geneName}\` to refresh.`);
+        }
         display.info("Running via WASM sandbox...");
         try {
             const { tryLoadBinding } = await import("../utils/binding.js");
             const binding = tryLoadBinding();
             if (binding) {
                 const wasmBytes = (0, node_fs_1.readFileSync)(wasmPath);
-                const phenoJson = (0, node_fs_1.readFileSync)((0, node_path_1.join)(geneDir, "phenotype.json"), "utf-8");
-                const execResult = binding.executeGene(wasmBytes, JSON.stringify(input), phenoJson);
+                const rawPhenotype = JSON.parse((0, node_fs_1.readFileSync)((0, node_path_1.join)(geneDir, "phenotype.json"), "utf-8"));
+                const { irHash: _strip, ...phenotypeForExec } = rawPhenotype;
+                const execResult = binding.executeGene(wasmBytes, JSON.stringify(input), JSON.stringify(phenotypeForExec), sandbox_defaults_js_1.DEFAULT_SANDBOX_CONSTRAINTS_JSON);
                 console.log();
                 if (execResult.success) {
                     display.success("Output:");

package/dist/commands/run.js.map

@@ -1 +1 @@
-{"version":3,"file":"run.js","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,yCAAoC;AACpC,qCAAmD;AACnD,yCAAiC;AACjC,6DAA+C;AAC/C,kDAAgE;AAChE,0EAAkE;AAErD,QAAA,UAAU,GAAG,IAAI,mBAAO,CAAC,KAAK,CAAC;KACzC,WAAW,CAAC,gCAAgC,CAAC;KAC7C,QAAQ,CAAC,aAAa,EAAE,sBAAsB,CAAC;KAC/C,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,EAAE,kBAAkB,CAAC;KACjE,MAAM,CAAC,WAAW,EAAE,gCAAgC,EAAE,KAAK,CAAC;KAC5D,MAAM,CAAC,cAAc,EAAE,yCAAyC,CAAC;KACjE,MAAM,CAAC,kBAAkB,EAAE,mDAAmD,EAAE,KAAK,CAAC;KACtF,MAAM,CACL,KAAK,EACH,QAAgB,EAChB,OAAsF,EACtF,EAAE;IACF,OAAO,CAAC,MAAM,CAAC,aAAa,QAAQ,EAAE,CAAC,CAAC;IACxC,IAAA,wCAAgB,EAAC,QAAQ,CAAC,CAAC;IAE3B,IAAI,IAAY,CAAC;IACjB,IAAI,CAAC;QACH,IAAI,GAAG,IAAA,0BAAc,GAAE,CAAC;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,KAAK,CAAC,qDAAqD,CAAC,CAAC;QACrE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,IAAA,sBAAU,EAAC,IAAI,CAAC,CAAC;IAChC,MAAM,OAAO,GAAG,IAAA,gBAAI,EAAC,IAAI,EAAE,MAAM,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IAEvD,IAAI,CAAC,IAAA,oBAAU,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,gBAAgB,CAAC,CAAC,EAAE,CAAC;QACjD,OAAO,CAAC,KAAK,CAAC,SAAS,QAAQ,kBAAkB,OAAO,EAAE,CAAC,CAAC;QAC5D,OAAO,CAAC,IAAI,CAAC,gCAAgC,CAAC,CAAC;QAC/C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,IAAI,SAAc,CAAC;IACnB,IAAI,CAAC;QACH,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAA,sBAAY,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,gBAAgB,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC;IACjF,CAAC;IAAC,OAAO,GAAQ,EAAE,CAAC;QAClB,OAAO,CAAC,KAAK,CAAC,iCAAiC,GAAG,GAAG,CAAC,OAAO,CAAC,CAAC;QAC/D,OAAO,CAAC,IAAI,CAAC,iDAAiD,CAAC,CAAC;QAChE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,IAAI,KAA8B,CAAC;IACnC,IAAI,CAAC;QACH,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IACpC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,KAAK,CAAC,wBAAwB,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC;QACxD,OAAO,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;QACtD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;QACpB,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;QACnC,OAAO,CAAC,QAAQ,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,IAAI,SAAS,CAAC,CAAC;QAC1D,OAAO,CAAC,QAAQ,CAAC,UAAU,EAAE,SAAS,CAAC,QAAQ,IAAI,SAAS,CAAC,CAAC;QAC9D,OAAO,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;QACjD,OAAO,CAAC,GAAG,EAAE,CAAC;IAChB,CAAC;IAED,MAAM,QAAQ,GAAG,IAAA,gBAAI,EAAC,OAAO,EAAE,cAAc,CAAC,CAAC;IAC/C,MAAM,UAAU,GAAG,IAAA,gBAAI,EAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAE7C,IAAI,IAAA,oBAAU,EAAC,QAAQ,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;QAC5C,OAAO,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC;QAC5C,IAAI,CAAC;YACH,MAAM,EAAE,cAAc,EAAE,GAAG,MAAM,MAAM,CAAC,qBAAqB,CAAC,CAAC;YAC/D,MAAM,OAAO,GAAG,cAAc,EAAE,CAAC;YACjC,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,SAAS,GAAG,IAAA,sBAAY,EAAC,QAAQ,CAAC,CAAC;gBACzC,MAAM,SAAS,GAAG,IAAA,sBAAY,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,gBAAgB,CAAC,EAAE,OAAO,CAAC,CAAC;gBACzE,MAAM,UAAU,GAAG,OAAO,CAAC,WAAW,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE,SAAS,CAAC,CAAC;gBACpF,OAAO,CAAC,GAAG,EAAE,CAAC;gBACd,IAAI,UAAU,CAAC,OAAO,EAAE,CAAC;oBACvB,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;oBAC3B,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;gBAC1D,CAAC;qBAAM,CAAC;oBACN,OAAO,CAAC,KAAK,CAAC,oBAAoB,GAAG,CAAC,UAAU,CAAC,YAAY,IAAI,SAAS,CAAC,CAAC,CAAC;oBAC7E,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAChB,OAAO;gBACT,CAAC;gBACD,OAAO,CAAC,EAAE,CAAC,UAAU,EAAE,GAAG,UAAU,CAAC,UAAU,IAAI,CAAC,CAAC;gBACrD,OAAO;YACT,CAAC;QACH,CAAC;QAAC,MAAM,CAAC,CAAC,6BAA6B,CAAC,CAAC;QACzC,OAAO,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;IACpE,CAAC;IAED,IAAI,IAAA,oBAAU,EAAC,UAAU,CAAC,EAAE,CAAC;QAC3B,MAAM,WAAW,GAAG,IAAA,oBAAU,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,sBAAsB,CAAC,CAAC,CAAC;QACtE,IAAI,WAAW,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC;YAC1C,OAAO,CAAC,KAAK,CAAC,+DAA+D,CAAC,CAAC;YAC/E,OAAO,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;YAChF,OAAO,CAAC,IAAI,CAAC,6CAA6C,GAAG,QAAQ,CAAC,CAAC;YACvE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAChB,OAAO;QACT,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC;QACvC,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,UAAU,CAAC,CAAC;YACrC,MAAM,EAAE,GAAG,GAAG,CAAC,OAAO,IAAI,GAAG,CAAC,OAAO,IAAI,GAAG,CAAC,IAAI,CAAC;YAClD,IAAI,OAAO,EAAE,KAAK,UAAU,EAAE,CAAC;gBAC7B,OAAO,CAAC,KAAK,CAAC,6DAA6D,CAAC,CAAC;gBAC7E,OAAO,CAAC,IAAI,CAAC,gFAAgF,CAAC,CAAC;gBAC/F,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBAChB,OAAO;YACT,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC;YAC/B,OAAO,CAAC,GAAG,EAAE,CAAC;YACd,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3B,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC/C,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,oBAAoB,GAAG,GAAG,CAAC,OAAO,CAAC,CAAC;YAClD,OAAO,CAAC,IAAI,CAAC,qCAAqC,CAAC,CAAC;YACpD,IAAI,OAAO,CAAC,OAAO,IAAI,GAAG,CAAC,KAAK,EAAE,CAAC;gBACjC,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;YAC3B,CAAC;YACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,0DAA0D,CAAC,CAAC;QAC1E,OAAO,CAAC,IAAI,CAAC,iCAAiC,GAAG,QAAQ,CAAC,CAAC;QAC3D,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC,CACF,CAAC"}
+{"version":3,"file":"run.js","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,yCAAoC;AACpC,qCAAmD;AACnD,yCAAiC;AACjC,6DAA+C;AAC/C,kDAAgE;AAChE,sEAAgF;AAChF,0EAAkE;AAErD,QAAA,UAAU,GAAG,IAAI,mBAAO,CAAC,KAAK,CAAC;KACzC,WAAW,CAAC,gCAAgC,CAAC;KAC7C,QAAQ,CAAC,aAAa,EAAE,sBAAsB,CAAC;KAC/C,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,EAAE,kBAAkB,CAAC;KACjE,MAAM,CAAC,WAAW,EAAE,gCAAgC,EAAE,KAAK,CAAC;KAC5D,MAAM,CAAC,cAAc,EAAE,yCAAyC,CAAC;KACjE,MAAM,CAAC,kBAAkB,EAAE,mDAAmD,EAAE,KAAK,CAAC;KACtF,MAAM,CACL,KAAK,EACH,QAAgB,EAChB,OAAsF,EACtF,EAAE;IACF,OAAO,CAAC,MAAM,CAAC,aAAa,QAAQ,EAAE,CAAC,CAAC;IACxC,IAAA,wCAAgB,EAAC,QAAQ,CAAC,CAAC;IAE3B,IAAI,IAAY,CAAC;IACjB,IAAI,CAAC;QACH,IAAI,GAAG,IAAA,0BAAc,GAAE,CAAC;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,KAAK,CAAC,6DAA6D,CAAC,CAAC;QAC7E,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,IAAA,sBAAU,EAAC,IAAI,CAAC,CAAC;IAChC,MAAM,OAAO,GAAG,IAAA,gBAAI,EAAC,IAAI,EAAE,MAAM,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IAEvD,IAAI,CAAC,IAAA,oBAAU,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,gBAAgB,CAAC,CAAC,EAAE,CAAC;QACjD,OAAO,CAAC,KAAK,CAAC,SAAS,QAAQ,kBAAkB,OAAO,EAAE,CAAC,CAAC;QAC5D,OAAO,CAAC,IAAI,CAAC,gCAAgC,CAAC,CAAC;QAC/C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,IAAI,SAAc,CAAC;IACnB,IAAI,CAAC;QACH,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAA,sBAAY,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,gBAAgB,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC;IACjF,CAAC;IAAC,OAAO,GAAQ,EAAE,CAAC;QAClB,OAAO,CAAC,KAAK,CAAC,iCAAiC,GAAG,GAAG,CAAC,OAAO,CAAC,CAAC;QAC/D,OAAO,CAAC,IAAI,CAAC,iDAAiD,CAAC,CAAC;QAChE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,IAAI,KAA8B,CAAC;IACnC,IAAI,CAAC;QACH,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IACpC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,KAAK,CAAC,wBAAwB,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC;QACxD,OAAO,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;QACtD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IAED,MAAM,gBAAgB,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,cAAc,CAAC,CAAC;IAEhE,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;QACpB,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;QACnC,OAAO,CAAC,QAAQ,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,IAAI,SAAS,CAAC,CAAC;QAC1D,OAAO,CAAC,QAAQ,CAAC,UAAU,EAAE,SAAS,CAAC,QAAQ,IAAI,SAAS,CAAC,CAAC;QAC9D,OAAO,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;QACjD,OAAO,CAAC,GAAG,EAAE,CAAC;IAChB,CAAC;IAED,MAAM,QAAQ,GAAG,IAAA,gBAAI,EAAC,OAAO,EAAE,cAAc,CAAC,CAAC;IAC/C,MAAM,UAAU,GAAG,IAAA,gBAAI,EAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAE7C,IAAI,IAAA,oBAAU,EAAC,QAAQ,CAAC,IAAI,gBAAgB,EAAE,CAAC;QAC7C,oEAAoE;QACpE,uDAAuD;QACvD,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,2BAA2B,CAAC,CAAC;QAClE,IAAI,WAAW,CAAC,QAAQ,EAAE,UAAU,CAAC,EAAE,CAAC;YACtC,OAAO,CAAC,IAAI,CACV,sFAAsF,QAAQ,gBAAgB,CAC/G,CAAC;QACJ,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC;QAC5C,IAAI,CAAC;YACH,MAAM,EAAE,cAAc,EAAE,GAAG,MAAM,MAAM,CAAC,qBAAqB,CAAC,CAAC;YAC/D,MAAM,OAAO,GAAG,cAAc,EAAE,CAAC;YACjC,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,SAAS,GAAG,IAAA,sBAAY,EAAC,QAAQ,CAAC,CAAC;gBACzC,MAAM,YAAY,GAAG,IAAI,CAAC,KAAK,CAAC,IAAA,sBAAY,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,gBAAgB,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC;gBACxF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,gBAAgB,EAAE,GAAG,YAAY,CAAC;gBAC7D,MAAM,UAAU,GAAG,OAAO,CAAC,WAAW,CACpC,SAAS,EACT,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EACrB,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,EAChC,sDAAgC,CACjC,CAAC;gBACF,OAAO,CAAC,GAAG,EAAE,CAAC;gBACd,IAAI,UAAU,CAAC,OAAO,EAAE,CAAC;oBACvB,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;oBAC3B,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;gBAC1D,CAAC;qBAAM,CAAC;oBACN,OAAO,CAAC,KAAK,CAAC,oBAAoB,GAAG,CAAC,UAAU,CAAC,YAAY,IAAI,SAAS,CAAC,CAAC,CAAC;oBAC7E,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAChB,OAAO;gBACT,CAAC;gBACD,OAAO,CAAC,EAAE,CAAC,UAAU,EAAE,GAAG,UAAU,CAAC,UAAU,IAAI,CAAC,CAAC;gBACrD,OAAO;YACT,CAAC;QACH,CAAC;QAAC,MAAM,CAAC,CAAC,6BAA6B,CAAC,CAAC;QACzC,OAAO,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;IACpE,CAAC;IAED,IAAI,IAAA,oBAAU,EAAC,UAAU,CAAC,EAAE,CAAC;QAC3B,MAAM,WAAW,GAAG,IAAA,oBAAU,EAAC,IAAA,gBAAI,EAAC,OAAO,EAAE,sBAAsB,CAAC,CAAC,CAAC;QACtE,IAAI,WAAW,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC;YAC1C,OAAO,CAAC,KAAK,CAAC,+DAA+D,CAAC,CAAC;YAC/E,OAAO,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;YAChF,OAAO,CAAC,IAAI,CAAC,6CAA6C,GAAG,QAAQ,CAAC,CAAC;YACvE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAChB,OAAO;QACT,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC;QACvC,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,UAAU,CAAC,CAAC;YACrC,MAAM,EAAE,GAAG,GAAG,CAAC,OAAO,IAAI,GAAG,CAAC,OAAO,IAAI,GAAG,CAAC,IAAI,CAAC;YAClD,IAAI,OAAO,EAAE,KAAK,UAAU,EAAE,CAAC;gBAC7B,OAAO,CAAC,KAAK,CAAC,6DAA6D,CAAC,CAAC;gBAC7E,OAAO,CAAC,IAAI,CAAC,gFAAgF,CAAC,CAAC;gBAC/F,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBAChB,OAAO;YACT,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC;YAC/B,OAAO,CAAC,GAAG,EAAE,CAAC;YACd,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3B,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC/C,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,oBAAoB,GAAG,GAAG,CAAC,OAAO,CAAC,CAAC;YAClD,OAAO,CAAC,IAAI,CAAC,qCAAqC,CAAC,CAAC;YACpD,IAAI,OAAO,CAAC,OAAO,I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package/dist/commands/test.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"test.d.ts","sourceRoot":"","sources":["../../src/commands/test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAYpC,eAAO,MAAM,WAAW,SA+VpB,CAAC"}
+{"version":3,"file":"test.d.ts","sourceRoot":"","sources":["../../src/commands/test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAapC,eAAO,MAAM,WAAW,SAuWpB,CAAC"}

package/dist/commands/test.js

@@ -46,6 +46,7 @@ const display = __importStar(require("../utils/display.js"));
 const config_js_1 = require("../utils/config.js");
 const project_root_js_1 = require("../utils/project-root.js");
 const binding_js_1 = require("../utils/binding.js");
+const sandbox_defaults_js_1 = require("../utils/sandbox-defaults.js");
 const network_gateway_js_1 = require("../runtime/network-gateway.js");
 const validate_gene_name_js_1 = require("../utils/validate-gene-name.js");
 exports.testCommand = new commander_1.Command("test")
@@ -150,7 +151,8 @@ exports.testCommand = new commander_1.Command("test")
         display.info("Test 6: WASM Sandbox — executeGene() Execution");
         try {
             const irWasm = (0, node_fs_1.readFileSync)(irWasmPath);
-            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotype));
+            const { irHash: _strip, ...phenotypeForExec } = phenotype;
+            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotypeForExec), sandbox_defaults_js_1.DEFAULT_SANDBOX_CONSTRAINTS_JSON);
             if (result.success) {
                 passed++;
                 display.success(`  executeGene() succeeded (${result.durationMs}ms, fuel: ${result.fuelConsumed})`);
@@ -303,7 +305,8 @@ exports.testCommand = new commander_1.Command("test")
         display.info("C1: Sandbox Execution Verification");
         if (hasIrWasm && binding) {
             const irWasm = (0, node_fs_1.readFileSync)(irWasmPath);
-            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotype));
+            const { irHash: _strip, ...phenotypeForExec } = phenotype;
+            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotypeForExec), sandbox_defaults_js_1.DEFAULT_SANDBOX_CONSTRAINTS_JSON);
             if (result.success && result.sandboxType === "wasm") {
                 passed++;
                 display.success("  Native gene executed through WASM sandbox");
@@ -320,7 +323,8 @@ exports.testCommand = new commander_1.Command("test")
         display.info("C2: Fuel Consumption Verification");
         if (hasIrWasm && binding) {
             const irWasm = (0, node_fs_1.readFileSync)(irWasmPath);
-            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotype));
+            const { irHash: _strip, ...phenotypeForExec } = phenotype;
+            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotypeForExec), sandbox_defaults_js_1.DEFAULT_SANDBOX_CONSTRAINTS_JSON);
             if (result.fuelConsumed > 0) {
                 passed++;
                 display.success(`  Fuel consumed: ${result.fuelConsumed} units`);
@@ -367,7 +371,8 @@ exports.testCommand = new commander_1.Command("test")
         display.info("C5: Fitness Score Computability");
         if (hasIrWasm && binding) {
             const irWasm = (0, node_fs_1.readFileSync)(irWasmPath);
-            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotype));
+            const { irHash: _strip, ...phenotypeForExec } = phenotype;
+            const result = binding.executeGene(irWasm, JSON.stringify(testInput), JSON.stringify(phenotypeForExec), sandbox_defaults_js_1.DEFAULT_SANDBOX_CONSTRAINTS_JSON);
             if (result.success && result.fuelConsumed > 0 && result.durationMs >= 0) {
                 passed++;
                 display.success("  All F(g) input metrics available");

package/dist/commands/test.js.map

@@ -1 +1 @@
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package/dist/commands/user-config.js

@@ -45,7 +45,7 @@ exports.userConfigCommand = new commander_1.Command("config")
     .action((key) => {
     if (!(0, user_config_js_1.isValidKey)(key)) {
         display.error(`Unknown config key: ${key}`);
-        display.hint("Valid keys: update-check, last-version");
+        display.hint("Valid keys: update-check, last-version, default-publish");
         process.exit(1);
     }
     display.kv(key, String((0, user_config_js_1.getUserConfigValue)(key)));
@@ -57,7 +57,7 @@ exports.userConfigCommand = new commander_1.Command("config")
     .action((key, value) => {
     if (!(0, user_config_js_1.isValidKey)(key)) {
         display.error(`Unknown config key: ${key}`);
-        display.hint("Valid keys: update-check, last-version");
+        display.hint("Valid keys: update-check, last-version, default-publish");
         process.exit(1);
     }
     (0, user_config_js_1.setUserConfigValue)(key, value);

package/dist/commands/user-config.js.map

@@ -1 +1 @@
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+{"version":3,"file":"user-config.js","sourceRoot":"","sources":["../../src/commands/user-config.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,yCAAoC;AACpC,6DAA+C;AAC/C,4DAA6G;AAEhG,QAAA,iBAAiB,GAAG,IAAI,mBAAO,CAAC,QAAQ,CAAC;KACnD,WAAW,CAAC,qCAAqC,CAAC;KAClD,UAAU,CACT,IAAI,mBAAO,CAAC,KAAK,CAAC;KACf,WAAW,CAAC,2BAA2B,CAAC;KACxC,QAAQ,CAAC,OAAO,EAAE,uCAAuC,CAAC;KAC1D,MAAM,CAAC,CAAC,GAAW,EAAE,EAAE;IACtB,IAAI,CAAC,IAAA,2BAAU,EAAC,GAAG,CAAC,EAAE,CAAC;QACrB,OAAO,CAAC,KAAK,CAAC,uBAAuB,GAAG,EAAE,CAAC,CAAC;QAC5C,OAAO,CAAC,IAAI,CAAC,yDAAyD,CAAC,CAAC;QACxE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IACD,OAAO,CAAC,EAAE,CAAC,GAAG,EAAE,MAAM,CAAC,IAAA,mCAAkB,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC;AACnD,CAAC,CAAC,CACL;KACA,UAAU,CACT,IAAI,mBAAO,CAAC,KAAK,CAAC;KACf,WAAW,CAAC,2BAA2B,CAAC;KACxC,QAAQ,CAAC,OAAO,EAAE,mBAAmB,CAAC;KACtC,QAAQ,CAAC,SAAS,EAAE,cAAc,CAAC;KACnC,MAAM,CAAC,CAAC,GAAW,EAAE,KAAa,EAAE,EAAE;IACrC,IAAI,CAAC,IAAA,2BAAU,EAAC,GAAG,CAAC,EAAE,CAAC;QACrB,OAAO,CAAC,KAAK,CAAC,uBAAuB,GAAG,EAAE,CAAC,CAAC;QAC5C,OAAO,CAAC,IAAI,CAAC,yDAAyD,CAAC,CAAC;QACxE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IACD,IAAA,mCAAkB,EAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IAC/B,OAAO,CAAC,OAAO,CAAC,GAAG,GAAG,MAAM,KAAK,EAAE,CAAC,CAAC;AACvC,CAAC,CAAC,CACL;KACA,UAAU,CACT,IAAI,mBAAO,CAAC,MAAM,CAAC;KAChB,WAAW,CAAC,+BAA+B,CAAC;KAC5C,MAAM,CAAC,GAAG,EAAE;IACX,MAAM,MAAM,GAAG,IAAA,+BAAc,GAAE,CAAC;IAEhC,OAAO,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,EAAE;QACpC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;QACrC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,OAAO,CAAC,IAAI,CAAC,wCAAwC,CAAC,CAAC;YACvD,OAAO;QACT,CAAC;QACD,OAAO,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC;QAChC,KAAK,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,OAAO,EAAE,CAAC;YAC7B,OAAO,CAAC,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;QAC3B,CAAC;IACH,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CACL,CAAC"}

package/dist/commands/versions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"versions.d.ts","sourceRoot":"","sources":["../../src/commands/versions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAMpC,eAAO,MAAM,eAAe,SAoExB,CAAC"}
+{"version":3,"file":"versions.d.ts","sourceRoot":"","sources":["../../src/commands/versions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAOpC,eAAO,MAAM,eAAe,SAsGxB,CAAC"}

package/dist/commands/versions.js

@@ -39,11 +39,42 @@ const display = __importStar(require("../utils/display.js"));
 const palette_js_1 = require("../utils/palette.js");
 const client_js_1 = require("../cloud/client.js");
 const validate_gene_name_js_1 = require("../utils/validate-gene-name.js");
+const gene_ref_js_1 = require("../cloud/gene-ref.js");
 exports.versionsCommand = new commander_1.Command("versions")
     .description("View version history chain for a gene")
-    .argument("<owner>", "gene owner username")
-    .argument("<gene-name>", "gene name")
-    .action(async (owner, geneName) => {
+    .argument("<ref-or-owner>", "@owner/name (preferred) OR owner username")
+    .argument("[gene-name]", "gene name (only when first arg is a bare owner)")
+    .action(async (refOrOwner, geneNameArg) => {
+    // Unify the user-facing ref syntax across all subcommands (Issue #50
+    // "Inconsistency surfaced"): historically `versions` was the lone
+    // outlier accepting `<owner> <gene-name>` as two positional args
+    // while everything else used `@owner/name`. Now we accept both:
+    //   rotifer versions @alice/foo        (preferred — single ref)
+    //   rotifer versions alice foo         (legacy — kept for compat)
+    let owner;
+    let geneName;
+    const ref = (0, gene_ref_js_1.parseGeneRef)(refOrOwner);
+    if (ref.kind === "ownerName") {
+        if (geneNameArg) {
+            display.error("Pass either '@owner/name' as a single argument OR '<owner> <gene-name>' as two arguments — not both.");
+            display.hint("Try: rotifer versions @" + ref.owner + "/" + ref.name);
+            process.exit(1);
+            return;
+        }
+        owner = ref.owner;
+        geneName = ref.name;
+    }
+    else if (geneNameArg) {
+        owner = refOrOwner;
+        geneName = geneNameArg;
+    }
+    else {
+        display.error("Provide either '@owner/name' (single argument) or '<owner> <gene-name>' (two arguments).");
+        display.hint("Try: rotifer versions @alice/my-gene");
+        display.hint("     rotifer versions alice my-gene");
+        process.exit(1);
+        return;
+    }
     (0, validate_gene_name_js_1.validateGeneName)(geneName);
     const s = display.spinner("Fetching version history...");
     try {