refactor: migrate from Bun.Glob to npm glob package

Replace Bun.Glob usage with a new Glob utility wrapper around the npm 'glob' package.
This moves us off Bun-specific APIs toward standard Node.js compatible solutions.

Changes:
- Add new src/util/glob.ts utility module with scan(), scanSync(), and match()
- Default include option is 'file' (only returns files, not directories)
- Add symlink option (default: false) to control symlink following
- Migrate all 12 files using Bun.Glob to use the new Glob utility
- Add comprehensive tests for the glob utility

Breaking changes:
- Removed support for include: 'dir' option (use include: 'all' and filter manually)
- symlink now defaults to false (was true in most Bun.Glob usages)

Files migrated:
- src/util/log.ts
- src/util/filesystem.ts
- src/tool/truncation.ts
- src/session/instruction.ts
- src/storage/json-migration.ts
- src/storage/storage.ts
- src/project/project.ts
- src/cli/cmd/tui/context/theme.tsx
- src/config/config.ts
- src/tool/registry.ts
- src/skill/skill.ts
- src/file/ignore.ts

packages/opencode/src/tool/registry.ts

@@ -27,16 +27,16 @@ import { LspTool } from "./lsp"
 import { Truncate } from "./truncation"
 import { PlanExitTool, PlanEnterTool } from "./plan"
 import { ApplyPatchTool } from "./apply_patch"
+import { Glob } from "../util/glob"
 
 export namespace ToolRegistry {
   const log = Log.create({ service: "tool.registry" })
 
   export const state = Instance.state(async () => {
     const custom = [] as Tool.Info[]
-    const glob = new Bun.Glob("{tool,tools}/*.{js,ts}")
 
     const matches = await Config.directories().then((dirs) =>
-      dirs.flatMap((dir) => [...glob.scanSync({ cwd: dir, absolute: true, followSymlinks: true, dot: true })]),
+      dirs.flatMap((dir) => Glob.scanSync("{tool,tools}/*.{js,ts}", { cwd: dir, absolute: true, dot: true })),
     )
     if (matches.length) await Config.waitForDependencies()
     for (const match of matches) {

packages/opencode/src/tool/truncation.ts

@@ -6,6 +6,7 @@ import { PermissionNext } from "../permission/next"
 import type { Agent } from "../agent/agent"
 import { Scheduler } from "../scheduler"
 import { Filesystem } from "../util/filesystem"
+import { Glob } from "../util/glob"
 
 export namespace Truncate {
   export const MAX_LINES = 2000
@@ -34,8 +35,7 @@ export namespace Truncate {
 
   export async function cleanup() {
     const cutoff = Identifier.timestamp(Identifier.create("tool", false, Date.now() - RETENTION_MS))
-    const glob = new Bun.Glob("tool_*")
-    const entries = await Array.fromAsync(glob.scan({ cwd: DIR, onlyFiles: true })).catch(() => [] as string[])
+    const entries = await Glob.scan("tool_*", { cwd: DIR, include: "file" }).catch(() => [] as string[])
     for (const entry of entries) {
       if (Identifier.timestamp(entry) >= cutoff) continue
       await fs.unlink(path.join(DIR, entry)).catch(() => {})