From 9872e53cca845276bd0af7cd6d4fc93e030f75bd Mon Sep 17 00:00:00 2001
From: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
Date: Mon, 12 Jan 2026 11:45:21 -0800
Subject: [PATCH 1/2] Set built JBrowse CLI version to the @jbrowse/core
 version

---
 .../external/fetch-jbrowse-bundle.mjs         | 55 +++++++++++++++----
 1 file changed, 44 insertions(+), 11 deletions(-)

diff --git a/jbrowse/resources/external/fetch-jbrowse-bundle.mjs b/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
index 04623fe0b..27366dbc2 100644
--- a/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
+++ b/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
@@ -1,5 +1,5 @@
 import { execSync } from 'node:child_process';
-import { existsSync, mkdirSync, copyFileSync, rmSync } from 'node:fs';
+import { existsSync, mkdirSync, copyFileSync, rmSync, readFileSync } from 'node:fs';
 import { join, resolve } from 'node:path';
 
 const ROOT = resolve('.');
@@ -7,6 +7,25 @@ const BUILD = join(ROOT, 'buildCli');
 const OUTDIR = join(ROOT, 'resources', 'external');
 const OUTFILE = join(OUTDIR, 'jbrowse.js');
 
+function getResolvedCoreVersion() {
+  // Prefer lockfile, fallback to node_modules
+  const lockPath = join(ROOT, 'package-lock.json');
+  if (existsSync(lockPath)) {
+    const lock = JSON.parse(readFileSync(lockPath, 'utf8'));
+    const v =
+      lock?.packages?.['node_modules/@jbrowse/core']?.version ||
+      lock?.dependencies?.['@jbrowse/core']?.version;
+    if (v) return v;
+  }
+
+  const corePkg = join(ROOT, 'node_modules', '@jbrowse', 'core', 'package.json');
+  if (existsSync(corePkg)) {
+    return JSON.parse(readFileSync(corePkg, 'utf8')).version;
+  }
+
+  throw new Error('Could not determine resolved @jbrowse/core version (no lockfile entry and no node_modules).');
+}
+
 async function extractTgz(tgzPath, cwd) {
   try {
     const mod = await import('tar').catch(() => null);
@@ -20,19 +39,36 @@ async function extractTgz(tgzPath, cwd) {
   execSync(`tar -xzf "${tgzPath}" -C "${cwd}"`, { stdio: 'inherit', shell: true });
 }
 
+function findCliEntrypoint(buildDir) {
+  const candidates = [
+    join(buildDir, 'package', 'bundle', 'index.js'),
+    join(buildDir, 'package', 'lib', 'index.js')
+  ];
+
+  for (const p of candidates) {
+    if (existsSync(p)) return p;
+  }
+
+  throw new Error(
+    `Could not find @jbrowse/cli entrypoint. Tried:\n` +
+    candidates.map(c => `  - ${c}`).join('\n')
+  );
+}
+
 async function main() {
   if (existsSync(BUILD)) rmSync(BUILD, { recursive: true, force: true });
   mkdirSync(BUILD, { recursive: true });
   mkdirSync(OUTDIR, { recursive: true });
 
-  console.log('Packing @jbrowse/cli (latest)…');
-  const out = execSync('npm pack @jbrowse/cli', {
+  const coreVersion = getResolvedCoreVersion();
+  const cliSpec = process.env.JBROWSE_CLI_VERSION || coreVersion;
+
+  console.log(`Packing @jbrowse/cli@${cliSpec} (core resolved: ${coreVersion})…`);
+  const out = execSync(`npm pack @jbrowse/cli@${cliSpec}`, {
     cwd: BUILD,
     stdio: ['ignore', 'pipe', 'inherit'],
     shell: true,
-  })
-    .toString()
-    .trim();
+  }).toString().trim();
 
   const tgz = join(BUILD, out);
   console.log(`Downloaded: ${tgz}`);
@@ -40,12 +76,9 @@ async function main() {
   console.log('Extracting tarball…');
   await extractTgz(tgz, BUILD);
 
-  const bundled = join(BUILD, 'package', 'bundle', 'index.js');
-  if (!existsSync(bundled)) {
-    throw new Error(`bundle/index.js not found at ${bundled}`);
-  }
+  const entry = findCliEntrypoint(BUILD);
 
-  copyFileSync(bundled, OUTFILE);
+  copyFileSync(entry, OUTFILE);
   console.log(`Copied bundle to ${OUTFILE}`);
 
   rmSync(BUILD, { recursive: true, force: true });

From e3e22c6c6ff0757d5c0abd35ba67e2719acee4a3 Mon Sep 17 00:00:00 2001
From: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
Date: Mon, 12 Jan 2026 14:26:18 -0800
Subject: [PATCH 2/2] Floor version to 3.6.0

---
 .../external/fetch-jbrowse-bundle.mjs         | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/jbrowse/resources/external/fetch-jbrowse-bundle.mjs b/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
index 27366dbc2..16a028199 100644
--- a/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
+++ b/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
@@ -26,6 +26,25 @@ function getResolvedCoreVersion() {
   throw new Error('Could not determine resolved @jbrowse/core version (no lockfile entry and no node_modules).');
 }
 
+function semverLt(a, b) {
+  const pa = String(a).match(/(\d+)\.(\d+)\.(\d+)/);
+  const pb = String(b).match(/(\d+)\.(\d+)\.(\d+)/);
+  if (!pa || !pb) return false;
+  for (let i = 1; i <= 3; i++) {
+    const da = Number(pa[i]);
+    const db = Number(pb[i]);
+    if (da !== db) return da < db;
+  }
+  return false;
+}
+
+function floorVersion(spec, min) {
+  const m = String(spec).match(/^(\^|~|>=)?\s*(\d+\.\d+\.\d+)(.*)$/);
+  if (!m) return spec;
+  const [, op = '', v, rest = ''] = m;
+  return semverLt(v, min) ? `${op}${min}${rest}` : spec;
+}
+
 async function extractTgz(tgzPath, cwd) {
   try {
     const mod = await import('tar').catch(() => null);
@@ -61,7 +80,7 @@ async function main() {
   mkdirSync(OUTDIR, { recursive: true });
 
   const coreVersion = getResolvedCoreVersion();
-  const cliSpec = process.env.JBROWSE_CLI_VERSION || coreVersion;
+  const cliSpec = floorVersion(process.env.JBROWSE_CLI_VERSION || coreVersion, '3.6.0');
 
   console.log(`Packing @jbrowse/cli@${cliSpec} (core resolved: ${coreVersion})…`);
   const out = execSync(`npm pack @jbrowse/cli@${cliSpec}`, {