diff --git a/README.md b/README.md
index abceb993..6ee1e3c8 100644
--- a/README.md
+++ b/README.md
@@ -79,13 +79,13 @@ Alternatively, you may prefer to run the remote script directly through
 
 #### Usage
 
-```
+````
 > molt --help
 Usage: molt <modules...>
 
 Description:
 
-  Check updates to dependencies in Deno modules
+  Check updates to dependencies in Deno modules and configuration files
 
 Options:
 
@@ -104,56 +104,48 @@ Options:
 
 Examples:
 
-  Check updates in a module:     molt deps.ts                               
+  Check import maps in a config: molt deno.json                             
+  Check imports in a module:     molt deps.ts                               
   Include multiple modules:      molt mod.ts lib.ts                         
   Target all .ts files:          molt ./**/*.ts                             
   Specify an import map:         molt mod.ts --import-map deno.json         
-  Ignore specific dependencies:  molt deps.ts --ignore=deno_graph,node_emoji
-  Only check deno_std:           molt deps.ts --only deno.land/std
-```
+  Ignore specified dependencies: molt deps.ts --ignore=deno_graph,node_emoji
+  Check deno_std only:           molt deps.ts --only deno.land/std          
 
 > [!Note]\
-> Molt CLI automatically uses import maps defined in `deno.json` or `deno.jsonc`
-> if available.\
-> You can't, however, use import maps as entrypoints.
+> Molt CLI automatically finds `deno.json` or `deno.jsonc` in the current
+> working directory or its parent directories and uses import maps defined in
+> the file if available.\
 
 #### Examples
 
 ##### Check for updates
 
 ```sh
-> molt mod.ts 
+> molt deno.json
+📦 @luca/flag 1.0.0 => 123.456.789
 📦 deno.land/std 0.200.0 => 123.456.789
-  lib.ts 0.200.0
-  mod.ts 0.200.0
-
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  mod.ts 0.50.0
-
-📦 node-emoji 2.0.0 => 123.456.789
-  mod.ts 2.0.0
-```
+📦 node-emoji 1.0.0 => 123.456.789
+````
 
 ##### Write changes to files
 
 ```sh
-> molt mod.ts --write
+> molt deno.json --write
     ...
-💾 lib.ts
-💾 mod.ts
+💾 deno.json
 ```
 
 ##### Commit changes to git
 
 ```sh
-> molt mod.ts --commit --pre-commit=test --prefix :package: --summary title.txt --report report.md
+> molt deno.json --commit --prefix :package:
     ...
+📝 :package: bump @luca/flag from 1.0.0 to 123.456.789
 📝 :package: bump deno.land/std from 0.200.0 to 123.456.789
 📝 :package: bump deno.land/x/deno_graph from 0.50.0 to 123.456.789
 📝 :package: bump node-emoji from 2.0.0 to 123.456.789
-
-📄 title.txt
-📄 report.md
 ```
 
 ## Compatibility with registries
diff --git a/cli.ts b/cli.ts
index 2a60794c..9f5a3f4f 100644
--- a/cli.ts
+++ b/cli.ts
@@ -1,6 +1,6 @@
 import { distinct, filterKeys, mapEntries } from "./lib/std/collections.ts";
 import { parse as parseJsonc } from "./lib/std/jsonc.ts";
-import { extname, relative } from "./lib/std/path.ts";
+import { relative } from "./lib/std/path.ts";
 import { colors, Command } from "./lib/x/cliffy.ts";
 import { $ } from "./lib/x/dax.ts";
 import { ensure, is } from "./lib/x/unknownutil.ts";
@@ -19,9 +19,12 @@ const { gray, yellow, bold, cyan } = colors;
 
 const main = new Command()
   .name("molt")
-  .description("Check updates to dependencies in Deno modules")
+  .description(
+    "Check updates to dependencies in Deno modules and configuration files",
+  )
   .versionOption("-v, --version", "Print version info.", versionCommand)
-  .example("Check updates in a module", "molt deps.ts")
+  .example("Check import maps in a config", "molt deno.json")
+  .example("Check imports in a module", "molt deps.ts")
   .example("Include multiple modules", "molt mod.ts lib.ts")
   .example("Target all .ts files", "molt ./**/*.ts")
   .option("--import-map <file:string>", "Specify import map file")
@@ -51,16 +54,16 @@ const main = new Command()
   .option("--summary <file:string>", "Write a summary of changes to file")
   .option("--report <file:string>", "Write a report of changes to file")
   .arguments("<modules...:string>")
-  .action(async function (options, ...entrypoints) {
+  .action(async function (options, ...files) {
     if (options.importMap) {
       if (await $.path(options.importMap).exists() === false) {
         console.error(`Import map ${options.importMap} does not exist.`);
         Deno.exit(1);
       }
     }
-    ensureJsFiles(entrypoints);
-    const updates = await collectUpdates(entrypoints, options);
-    printUpdates(updates);
+    ensureFiles(files);
+    const updates = await collectUpdates(files, options);
+    printUpdates(files, updates);
     if (options.write) {
       return writeUpdates(updates, options);
     }
@@ -102,7 +105,6 @@ async function collectUpdates(
     const updates = await Promise.all(
       entrypoints.map(async (entrypoint) =>
         await collect(entrypoint, {
-          findImportMap: options.importMap === undefined,
           ignore: options.ignore
             ? (dep) => options.ignore!.some((it) => dep.name.includes(it))
             : undefined,
@@ -149,7 +151,10 @@ async function getTasks() {
 
 const toRelativePath = (path: string) => relative(Deno.cwd(), path);
 
-function printUpdates(updates: DependencyUpdate[]) {
+function printUpdates(
+  files: string[],
+  updates: DependencyUpdate[],
+) {
   const dependencies = new Map<string, DependencyUpdate[]>();
   for (const u of updates) {
     const list = dependencies.get(u.to.name) ?? [];
@@ -157,19 +162,22 @@ function printUpdates(updates: DependencyUpdate[]) {
     dependencies.set(u.to.name, list);
   }
   let count = 0;
+  const nWrites = distinct(updates.map((u) => u.referrer)).length;
   for (const [name, list] of dependencies.entries()) {
     const froms = distinct(list.map((u) => u.from.version)).join(", ");
     console.log(
       `📦 ${bold(name)} ${yellow(froms)} => ${yellow(list[0].to.version)}`,
     );
-    distinct(
-      list.map((u) => {
-        const source = toRelativePath(u.map?.source ?? u.referrer);
-        return `  ${source} ` + gray(u.from.version ?? "");
-      }),
-    ).forEach((line) => console.log(line));
-    if (++count < dependencies.size) {
-      console.log();
+    if (files.length > 1 || nWrites > 1) {
+      distinct(
+        list.map((u) => {
+          const source = toRelativePath(u.map?.source ?? u.referrer);
+          return `  ${source} ` + gray(u.from.version ?? "");
+        }),
+      ).forEach((line) => console.log(line));
+      if (++count < dependencies.size) {
+        console.log();
+      }
     }
   }
 }
@@ -271,17 +279,14 @@ async function runTask([name, args]: [string, string[]]) {
   }
 }
 
-function ensureJsFiles(paths: string[]) {
+function ensureFiles(paths: string[]) {
   for (const path of paths) {
-    if (!["", ".js", ".ts", ".jsx", ".tsx"].includes(extname(path))) {
-      throw new Error(`❌ file must be javascript or typescript: "${path}"`);
-    }
     try {
       if (!Deno.statSync(path).isFile) {
-        throw new Error(`❌ not a file: "${path}"`);
+        throw new Error(`Not a valid file: "${path}"`);
       }
     } catch {
-      throw new Error(`❌ path does not exist: "${path}"`);
+      throw new Error(`Path does not exist: "${path}"`);
     }
   }
 }
diff --git a/deno.json b/deno.json
index b1b65ef8..5e5059eb 100644
--- a/deno.json
+++ b/deno.json
@@ -4,7 +4,7 @@
     "lock": "deno task -q cache --lock-write && git add deno.lock",
     "check": "deno check ./*.ts ./lib/*.ts ./test/integration/*.ts",
     "test": "NO_COLOR=1 deno test -A --no-check ./lib",
-    "all": "deno fmt && deno lint && deno task -q check && deno task lock && deno task -q test",
+    "pre-commit": "deno fmt && deno lint && deno task -q check && deno task lock && deno task -q test",
     "integration": "NO_COLOR=1 deno test --no-lock -A ./test/integration/*.ts",
     "run": "deno run --allow-env --allow-read --allow-net --allow-write=. --allow-run=git,deno cli.ts",
     "update": "deno run --allow-env --allow-read --allow-write --allow-net=deno.land,registry.npmjs.org --allow-run=git,deno ./cli.ts ./lib/*/*.ts",
diff --git a/lib/file.ts b/lib/file.ts
index bf509f61..8f4f5dfc 100644
--- a/lib/file.ts
+++ b/lib/file.ts
@@ -1,8 +1,7 @@
-import { parse as parseJsonc } from "./std/jsonc.ts";
 import { detectEOL } from "./std/fs.ts";
 import { toUrl } from "./dependency.ts";
 import { type DependencyUpdate } from "./update.ts";
-import { ImportMapJson } from "./import_map.ts";
+import { readImportMapJson } from "./import_map.ts";
 
 /**
  * Write the given array of DependencyUpdate to files.
@@ -27,16 +26,21 @@ export function writeAll(
   return write(associateByFile(updates), options);
 }
 
+type FileKind = "module" | "import_map";
+
 /**
  * A collection of updates to dependencies associated with a file.
  */
-export interface FileUpdate {
-  /** The full path to the file being updated. */
+export interface FileUpdate<
+  Kind extends FileKind = FileKind,
+> {
+  /** The full path to the file being updated.
+   * @example "/path/to/mod.ts" */
   path: string;
   /** The type of the file being updated. */
-  kind: "module" | "import_map";
+  kind: Kind;
   /** The updates to dependencies associated with the file. */
-  dependencies: DependencyUpdate[];
+  dependencies: DependencyUpdate<Kind extends "import_map" ? true : false>[];
 }
 
 /**
@@ -83,16 +87,16 @@ function _write(
 ) {
   switch (update.kind) {
     case "module":
-      return writeToModule(update);
+      return writeToModule(update as FileUpdate<"module">);
     case "import_map":
-      return writeToImportMap(update);
+      return writeToImportMap(update as FileUpdate<"import_map">);
   }
 }
 
 async function writeToModule(
-  update: FileUpdate,
+  update: FileUpdate<"module">,
 ) {
-  const lineToDependencyMap = new Map<number, DependencyUpdate>(
+  const lineToDependencyMap = new Map(
     update.dependencies.map((
       dependency,
     ) => [dependency.code.span.start.line, dependency]),
@@ -121,12 +125,11 @@ async function writeToModule(
 
 async function writeToImportMap(
   /** The dependency update to apply. */
-  update: FileUpdate,
+  update: FileUpdate<"import_map">,
 ) {
-  const content = await Deno.readTextFile(update.path);
-  const json = parseJsonc(content) as unknown as ImportMapJson;
+  const json = await readImportMapJson(update.path);
   for (const dependency of update.dependencies) {
-    json.imports[dependency.map!.key!] = toUrl(dependency.to);
+    json.imports[dependency.map.key] = toUrl(dependency.to);
   }
   await Deno.writeTextFile(update.path, JSON.stringify(json, null, 2));
 }
diff --git a/lib/file_test.ts b/lib/file_test.ts
index c8c64edd..9f90f56c 100644
--- a/lib/file_test.ts
+++ b/lib/file_test.ts
@@ -58,7 +58,7 @@ WriteTextFileStub.create(fs);
 async function test(path: string, name = toName(path)) {
   const updates = await DependencyUpdate.collect(
     new URL(path, import.meta.url),
-    { findImportMap: true },
+    { cwd: new URL(dirname(path), import.meta.url) },
   );
   const results = associateByFile(updates);
 
diff --git a/lib/import_map.ts b/lib/import_map.ts
index e82ec019..12aeb060 100644
--- a/lib/import_map.ts
+++ b/lib/import_map.ts
@@ -2,18 +2,18 @@ import { assertEquals } from "./std/assert.ts";
 import { maxBy } from "./std/collections.ts";
 import { parse as parseJsonc } from "./std/jsonc.ts";
 import { type ImportMapJson, parseFromJson } from "./x/import_map.ts";
-import { is } from "./x/unknownutil.ts";
+import { ensure, is } from "./x/unknownutil.ts";
 import { toPath } from "./path.ts";
 
 export type { ImportMapJson };
 
-export interface ImportMapResolveResult {
+export interface ImportMapResolveResult<HasKey extends boolean = boolean> {
   /** The fully-resolved URL string of the import specifier. */
   resolved: string;
   /** The key of the import map that matched with the import specifier. */
-  key?: string;
+  key: HasKey extends true ? string : undefined;
   /** The mapped value by the import map corresponding to the key. */
-  value?: string;
+  value: HasKey extends true ? string : undefined;
 }
 
 export interface ImportMap {
@@ -45,6 +45,20 @@ const isImportMapReferrer = is.ObjectOf({
   importMap: is.String,
 });
 
+/**
+ * Read and parse a JSON including import maps from the given file path or URL.
+ */
+export async function readImportMapJson(
+  url: string | URL,
+): Promise<ImportMapJson> {
+  const data = await Deno.readTextFile(url);
+  try {
+    return ensure(parseJsonc(data), isImportMapJson);
+  } catch {
+    throw new SyntaxError(`${url} does not have a valid import map`);
+  }
+}
+
 /**
  * Read an import map from the given file path or URL.
  * @param url - The URL of the import map.
@@ -91,7 +105,8 @@ export async function readFromJson(
       }
       return {
         resolved,
-        ...replacement,
+        key: replacement?.key,
+        value: replacement?.value,
       };
     },
     resolveInner: inner.resolve.bind(inner),
diff --git a/lib/import_map_test.ts b/lib/import_map_test.ts
index a920fe92..757dd36d 100644
--- a/lib/import_map_test.ts
+++ b/lib/import_map_test.ts
@@ -69,6 +69,8 @@ describe("resolve()", () => {
       {
         resolved:
           new URL("../test/data/import_map/lib.ts", import.meta.url).href,
+        key: undefined,
+        value: undefined,
       },
     );
   });
diff --git a/lib/update.ts b/lib/update.ts
index 4923e48c..65eefb3e 100644
--- a/lib/update.ts
+++ b/lib/update.ts
@@ -1,5 +1,5 @@
 import { distinct } from "./std/collections.ts";
-import { dirname, fromFileUrl } from "./std/path.ts";
+import { fromFileUrl } from "./std/path.ts";
 import {
   createGraph,
   type CreateGraphOptions,
@@ -11,21 +11,25 @@ import { findFileUp, toPath, toUrl } from "./path.ts";
 import {
   ImportMap,
   ImportMapResolveResult,
+  readImportMapJson,
   tryReadFromJson,
 } from "./import_map.ts";
 import {
   type Dependency,
   parse,
   resolveLatestVersion,
+  toUrl as dependencyToUrl,
   type UpdatedDependency,
 } from "./dependency.ts";
 
 type DependencyJson = NonNullable<ModuleJson["dependencies"]>[number];
 
+type If<T extends boolean, A, B> = T extends true ? A : B;
+
 /**
  * Representation of an update to a dependency.
  */
-export interface DependencyUpdate {
+export interface DependencyUpdate<IsMapped extends boolean = boolean> {
   /** Properties of the dependency being updated. */
   from: Dependency;
   /** Properties of the updated dependency. */
@@ -37,17 +41,21 @@ export interface DependencyUpdate {
   code: {
     /** The original specifier of the dependency appeared in the code. */
     specifier: string;
-    span: NonNullable<DependencyJson["code"]>["span"];
+    span: If<IsMapped, undefined, NonNullable<DependencyJson["code"]>["span"]>;
   };
   /** The full path to the module that imports the dependency.
    * @example "/path/to/mod.ts" */
   referrer: string;
   /** Information about the import map used to resolve the dependency. */
-  map?: {
-    /** The full path to the import map used to resolve the dependency.
-     * @example "/path/to/import_map.json" */
-    source: string;
-  } & ImportMapResolveResult;
+  map: If<
+    IsMapped,
+    {
+      /** The full path to the import map used to resolve the dependency.
+       * @example "/path/to/import_map.json" */
+      source: string;
+    } & ImportMapResolveResult<true>,
+    undefined
+  >;
 }
 
 class DenoGraph {
@@ -63,9 +71,18 @@ class DenoGraph {
 }
 
 export interface CollectOptions {
+  /**
+   * The working directory to resolve relative paths.
+   * If not specified, the current working directory is used.
+   * At present, this option is only used to find the import map.
+   *
+   * @example "/path/to/project"
+   */
+  cwd?: string | URL;
   /**
    * The path to the import map used to resolve dependencies.
-   * If not specified, deno.json or deno.jsonc in the root directory of the module is used.
+   * If not specified, molt will automatically find deno.json or deno.jsonc
+   * in the current working directory or parent directories.
    *
    * @example
    * ```ts
@@ -76,10 +93,6 @@ export interface CollectOptions {
    * ```
    */
   importMap?: string | URL;
-  /**
-   * If true, the import map is searched for in the parent directories of the first module specified.
-   */
-  findImportMap?: boolean;
   /**
    * A function to filter out dependencies.
    *
@@ -107,10 +120,23 @@ export interface CollectOptions {
 }
 
 /**
- * Collect dependencies from the given module(s).
- * @param from - The path(s) to the module(s) to collect dependencies from.
+ * Collect dependencies from the given module(s) or Deno configuration file(s).
+ * Local submodules are also checked recursively.
+ *
+ * @param from - The path(s) to the file(s) to collect dependencies from.
  * @param options - Options to customize the behavior.
  * @returns The list of dependencies.
+ *
+ * @example
+ * ```ts
+ * collect("mod.ts")
+ * // -> Collect dependencies from mod.ts and its local submodules.
+ * ```
+ * @example
+ * ```ts
+ * collect("deno.json")
+ * // -> Collect dependencies from the import map specified in deno.json
+ * ```
  */
 export async function collect(
   from: string | URL | (string | URL)[],
@@ -120,9 +146,7 @@ export async function collect(
   const urls = froms.map((path) => toUrl(path));
 
   const importMapPath = options.importMap ??
-    (options.findImportMap
-      ? await findFileUp(dirname(urls[0]), "deno.json", "deno.jsonc")
-      : undefined);
+    await findFileUp(options.cwd ?? Deno.cwd(), "deno.json", "deno.jsonc");
 
   const importMap = importMapPath
     ? await tryReadFromJson(toUrl(importMapPath))
@@ -135,18 +159,26 @@ export async function collect(
   });
 
   const updates: DependencyUpdate[] = [];
-  await Promise.all(
-    graph.modules.flatMap((m) =>
-      m.dependencies?.map(async (dependency) => {
-        const update = await create(
-          dependency,
-          m.specifier,
-          { ...options, importMap },
-        );
-        return update ? updates.push(update) : undefined;
-      })
-    ),
-  );
+  await Promise.all([
+    ...graph.modules
+      .filter((m) => m.kind === "esm")
+      .flatMap((m) =>
+        m.dependencies?.map(async (dependency) => {
+          const update = await _createDependencyUpdate(
+            dependency,
+            m.specifier,
+            { ...options, importMap },
+          );
+          return update ? updates.push(update) : undefined;
+        })
+      ),
+    ...graph.modules
+      .filter((m) => m.kind === "asserted" && m.mediaType === "Json")
+      .map(async (m) => {
+        const results = await _collectFromImportMap(m.specifier, options);
+        updates.push(...results);
+      }),
+  ]);
   return updates.sort((a, b) => a.to.name.localeCompare(b.to.name));
 }
 
@@ -157,6 +189,7 @@ const load: NonNullable<CreateGraphOptions["load"]> = async (
   switch (url.protocol) {
     case "node:":
     case "npm:":
+    case "jsr:":
       return {
         kind: "external",
         specifier,
@@ -181,7 +214,7 @@ const load: NonNullable<CreateGraphOptions["load"]> = async (
  * @param options - Options to customize the behavior.
  * @returns The created DependencyUpdate.
  */
-async function create(
+async function _createDependencyUpdate(
   dependencyJson: DependencyJson,
   referrer: string,
   options?: Pick<CollectOptions, "ignore" | "only"> & {
@@ -201,7 +234,7 @@ async function create(
   const mapped = options?.importMap?.resolve(
     dependencyJson.specifier,
     referrer,
-  );
+  ) as ImportMapResolveResult<true> | undefined;
   const dependency = parse(new URL(mapped?.value ?? specifier));
   if (options?.ignore?.(dependency)) {
     return;
@@ -239,6 +272,50 @@ async function create(
   };
 }
 
+async function _collectFromImportMap(
+  specifier: ModuleJson["specifier"],
+  options: Pick<CollectOptions, "ignore" | "only">,
+): Promise<DependencyUpdate[]> {
+  const json = await readImportMapJson(new URL(specifier));
+  const updates: DependencyUpdate[] = [];
+  await Promise.all(
+    Object.entries(json.imports).map(
+      async ([key, value]): Promise<DependencyUpdate | undefined> => {
+        if (!URL.canParse(value)) {
+          return;
+        }
+        const dependency = parse(new URL(value));
+        if (options.ignore?.(dependency)) {
+          return;
+        }
+        if (options.only && !options.only(dependency)) {
+          return;
+        }
+        const latest = await resolveLatestVersion(dependency);
+        if (!latest || latest.version === dependency.version) {
+          return;
+        }
+        updates.push({
+          from: dependency,
+          to: latest,
+          code: {
+            specifier: value,
+            span: undefined,
+          },
+          referrer: toPath(specifier),
+          map: {
+            source: toPath(specifier),
+            resolved: value,
+            key,
+            value: dependencyToUrl(latest),
+          },
+        });
+      },
+    ),
+  );
+  return updates;
+}
+
 export type VersionChange = {
   from?: string;
   to: string;
diff --git a/lib/update_test.ts b/lib/update_test.ts
index 236b1462..d21572fb 100644
--- a/lib/update_test.ts
+++ b/lib/update_test.ts
@@ -1,19 +1,29 @@
+import { dirname } from "./std/path.ts";
 import { assertEquals, assertThrows } from "./std/assert.ts";
 import { filterKeys } from "./std/collections.ts";
 import { basename } from "./std/path.ts";
 import { assertSnapshot } from "./testing.ts";
 import { LatestSemVerStub } from "./testing.ts";
+import { readImportMapJson } from "./import_map.ts";
 import { collect, DependencyUpdate, getVersionChange } from "./update.ts";
 
-const test = (path: string, name = basename(path)) =>
-  Deno.test("collect - " + name, async (t) => {
-    const updates = await collect(new URL(path, import.meta.url), {
-      findImportMap: true,
-    });
-    for (const update of updates) {
-      await assertUpdateSnapshot(t, update);
-    }
-  });
+function test(
+  path: string,
+  name = basename(path),
+  variation?: string,
+) {
+  Deno.test(
+    "collect - " + (variation ? `${name} - ${variation}` : name),
+    async (t) => {
+      const updates = await collect(new URL(path, import.meta.url), {
+        cwd: new URL(dirname(path), import.meta.url),
+      });
+      for (const update of updates) {
+        await assertUpdateSnapshot(t, update);
+      }
+    },
+  );
+}
 
 async function assertUpdateSnapshot(
   t: Deno.TestContext,
@@ -29,6 +39,15 @@ async function assertUpdateSnapshot(
   );
 }
 
+async function hasImportMap(url: URL) {
+  try {
+    await readImportMapJson(url);
+    return true;
+  } catch {
+    return false;
+  }
+}
+
 const LATEST = "123.456.789";
 LatestSemVerStub.create(LATEST);
 
@@ -45,8 +64,20 @@ for await (
         new URL("../test/data/" + testCase.name, import.meta.url),
       )
     ) {
-      if (entry.isFile && entry.name === "mod.ts") {
-        test(`../test/data/${testCase.name}/mod.ts`, testCase.name);
+      if (
+        entry.isFile && entry.name === "mod.ts" ||
+        entry.name.endsWith(".json") && await hasImportMap(
+            new URL(
+              `../test/data/${testCase.name}/${entry.name}`,
+              import.meta.url,
+            ),
+          )
+      ) {
+        test(
+          `../test/data/${testCase.name}/${entry.name}`,
+          testCase.name,
+          entry.name,
+        );
       }
     }
   }
diff --git a/test/data/import_map/deno.json b/test/data/import_map/deno.json
index 0c8ebcd8..6a32c256 100644
--- a/test/data/import_map/deno.json
+++ b/test/data/import_map/deno.json
@@ -3,6 +3,7 @@
     "std/": "https://deno.land/std@0.200.0/",
     "deno_graph": "https://deno.land/x/deno_graph@0.50.0/mod.ts",
     "node-emoji": "npm:node-emoji@1.0.0",
+    "flag": "jsr:@luca/flag@1.0.0",
     "/": "./"
   }
 }
diff --git a/test/data/import_map/mod.ts b/test/data/import_map/mod.ts
index 06d1d826..39afe7b3 100644
--- a/test/data/import_map/mod.ts
+++ b/test/data/import_map/mod.ts
@@ -1,4 +1,5 @@
 import { assert } from "std/assert.ts";
 import { createGraph } from "deno_graph";
 import { emojify } from "node-emoji";
+import { printProgress } from "flag";
 import { noop } from "/noop.ts";
diff --git a/test/data/multiple_imports.ts b/test/data/multiple_imports.ts
index d46da302..da326cfa 100644
--- a/test/data/multiple_imports.ts
+++ b/test/data/multiple_imports.ts
@@ -1,3 +1,4 @@
 import { assert } from "https://deno.land/std@0.200.0/assert/assert.ts";
 import { createGraph } from "https://deno.land/x/deno_graph@0.50.0/mod.ts";
 import emoji from "npm:node-emoji@2.0.0";
+import { printProgress } from "jsr:@luca/flag@1.0.0";
diff --git a/test/integration/cli.ts b/test/integration/cli.ts
index 307ecca7..9ed5c216 100644
--- a/test/integration/cli.ts
+++ b/test/integration/cli.ts
@@ -1,29 +1,86 @@
 import { assertEquals } from "../../lib/std/assert.ts";
 import { stripAnsiCode } from "../../lib/std/fmt.ts";
+import { join } from "../../lib/std/path.ts";
 import { assertSnapshot } from "../../lib/testing.ts";
 
-function stringify(data: Uint8Array) {
-  const decoder = new TextDecoder();
-  let text = decoder.decode(data);
-  if (Deno.build.os === "windows") {
-    text = text
-      .replace(/\r\n/g, "\n")
-      .replace(/\\/g, "/");
-  }
-  return stripAnsiCode(text);
-}
+// basic commands
+molt("", { code: 2 });
+molt("--help");
+molt("--version");
+
+// single file
+molt("not_exist.ts", { code: 1 });
+molt("import.ts");
+
+// special registries
+molt("jsr.ts");
+
+// with import maps
+molt("mod.ts", { cwd: "import_map" });
+molt("mod.ts --import-map deno.json", { cwd: "import_map" });
+
+// --ignore and --only
+molt("multiple_imports.ts --ignore node-emoji");
+molt("multiple_imports.ts --ignore=deno_graph,node-emoji");
+molt("multiple_imports.ts --only deno.land/std");
+molt("multiple_imports.ts --only=deno.land/std,deno_graph");
+molt("multiple_imports.ts --only deno.land --ignore deno_graph");
+
+// --write
+molt("mod.ts --write", { cwd: "multiple_modules" });
+molt(
+  "mod.ts --write --summary title.txt --report body.md",
+  { cwd: "multiple_modules" },
+);
+
+// --commit
+molt("mod.ts --commit", { cwd: "multiple_modules" });
+molt("mod.ts --commit --prefix :package:", { cwd: "multiple_modules" });
+molt(
+  "mod.ts --commit --pre-commit=fmt --post-commit=lint",
+  { cwd: "multiple_modules" },
+);
+molt(
+  "mod.ts --commit --summary title.txt --report body.md",
+  { cwd: "multiple_modules" },
+);
+molt(
+  "mod.ts --commit --summary title.txt --pre-commit=fmt",
+  { cwd: "multiple_modules" },
+);
+
+// deno.json
+molt("deno.json", { cwd: "import_map" });
+molt("deno.json --write", { cwd: "import_map" });
+molt("deno.json --commit --prefix :package:", { cwd: "import_map" });
+
+//-----------------------
+// Test implementation
+//-----------------------
+
+const BIN = new URL("../../cli.ts", import.meta.url).pathname;
+const DATA = new URL("../data", import.meta.url).pathname;
+
+function molt(line: string, opts?: {
+  cwd?: string;
+  code?: number;
+}) {
+  const args = line.length > 0 ? line.split(" ") : [];
+
+  const name = "cli - " + (opts?.cwd ? opts.cwd + " - " : "") +
+    '"' + ["molt"].concat(args).join(" ") + '"';
 
-function test(cmd: string, code = 0) {
-  const [, ...args] = cmd.split(" ");
-  Deno.test(cmd, async (t) => {
+  Deno.test(name, async (t) => {
     const output = await new Deno.Command("deno", {
-      args: ["run", "-A", "./cli.ts", ...args],
+      args: ["run", "-A", BIN, ...args],
       env: { MOLT_TEST: "1" },
+      cwd: join(DATA, opts?.cwd ? `/${opts?.cwd}` : ""),
     }).output();
+
     const stdout = stringify(output.stdout);
     const stderr = stringify(output.stderr);
     try {
-      assertEquals(output.code, code);
+      assertEquals(output.code, opts?.code ?? 0);
     } catch (err) {
       console.error(stdout);
       console.error(stderr);
@@ -34,46 +91,13 @@ function test(cmd: string, code = 0) {
   });
 }
 
-const dir = "test/data";
-
-test("molt", 2);
-test("molt --help");
-test("molt --version");
-
-test(`molt not_exist.ts`, 1);
-test(`molt ${dir}/import.ts`);
-
-test(`molt ${dir}/jsr.ts`);
-
-test(`molt ${dir}/import_map/mod.ts`);
-test(`molt ${dir}/import_map/mod.ts --import-map ${dir}/import_map/deno.json`);
-test(`molt ${dir}/import_map/deno.json`, 1);
-test(
-  `molt ${dir}/import_map/mod.ts --import-map not_exist.json`,
-  1,
-);
-
-test(`molt ${dir}/multiple_imports.ts --ignore node-emoji`);
-test(`molt ${dir}/multiple_imports.ts --ignore=deno_graph,node-emoji`);
-
-test(`molt ${dir}/multiple_imports.ts --only deno.land/std`);
-test(`molt ${dir}/multiple_imports.ts --only=deno.land/std,deno_graph`);
-
-test(`molt ${dir}/multiple_imports.ts --only deno.land --ignore deno_graph`);
-
-test(`molt ${dir}/multiple_modules/mod.ts --write`);
-test(
-  `molt ${dir}/multiple_modules/mod.ts --write --summary title.txt --report body.md`,
-);
-
-test(`molt ${dir}/multiple_modules/mod.ts --commit`);
-test(`molt ${dir}/multiple_modules/mod.ts --commit --prefix :package:`);
-test(
-  `molt ${dir}/multiple_modules/mod.ts --commit --pre-commit=fmt --post-commit=lint`,
-);
-test(
-  `molt ${dir}/multiple_modules/mod.ts --commit --summary title.txt --report body.md`,
-);
-test(
-  `molt ${dir}/multiple_modules/mod.ts --commit --summary title.txt --pre-commit=fmt`,
-);
+function stringify(data: Uint8Array) {
+  const decoder = new TextDecoder();
+  let text = decoder.decode(data);
+  if (Deno.build.os === "windows") {
+    text = text
+      .replace(/\r\n/g, "\n")
+      .replace(/\\/g, "/");
+  }
+  return stripAnsiCode(text);
+}
diff --git a/test/integration/registries.ts b/test/integration/registries.ts
index b079f3c3..6478cf94 100644
--- a/test/integration/registries.ts
+++ b/test/integration/registries.ts
@@ -17,37 +17,35 @@ const SPECS = [
   ],
   [
     "npm:",
-    "npm:preact@10.5.5",
+    "npm:preact@10.19.0",
   ],
   [
     "jsr:",
-    "jsr:@std/semver@0.210.0",
+    "jsr:@std/jsonc@0.210.0",
   ],
   [
     "cdn.jsdelivr.net/npm",
-    "https://cdn.jsdelivr.net/npm/preact@10.5.5",
+    "https://cdn.jsdelivr.net/npm/preact@10.19.0",
   ],
   [
     "cdn.jsdelivr.net/gh",
-    "https://cdn.jsdelivr.net/gh/hasundue/molt@e4509a9/lib/path.ts",
+    "https://cdn.jsdelivr.net/gh/hasundue/molt@8a4a9a7/lib/path.ts",
   ],
   [
     "cdn.skypack.dev",
-    "https://cdn.skypack.dev/preact@10.5.5",
+    "https://cdn.skypack.dev/preact@10.19.0",
   ],
   [
     "ga.jspm.io",
     "https://ga.jspm.io/npm:lit-html@2.7.0/development/is-server.js",
   ],
-  /**
   [
     "esm.run",
-    "https://esm.run/preact@10.5.5",
+    "https://esm.run/preact@10.19.0",
   ],
-  */
   [
     "esm.sh",
-    "https://esm.sh/preact@10.5.5",
+    "https://esm.sh/preact@10.19.0",
   ],
   [
     "x.nest.land",
@@ -55,32 +53,24 @@ const SPECS = [
   ],
   [
     "pax.deno.dev",
-    "https://pax.deno.dev/hasundue/molt@e4509a9/lib/path.ts",
+    "https://pax.deno.dev/hasundue/molt@8a4a9a7/lib/path.ts",
   ],
   [
     "raw.githubusercontent.com",
-    "https://raw.githubusercontent.com/hasundue/molt/e4509a9/lib/path.ts",
+    "https://raw.githubusercontent.com/hasundue/molt/8a4a9a7/lib/path.ts",
   ],
   [
     "unpkg.com",
-    "https://unpkg.com/preact@10.5.5",
+    "https://unpkg.com/preact@10.19.0",
   ],
 ] satisfies RegistryTestSpec[];
 
 for (const spec of SPECS) {
-  const name = spec[0];
+  const name = "registry - " + spec[0];
 
   Deno.test(name, async (t) => {
     const assert = (it: unknown) => assertSnapshot(t, it !== undefined);
 
-    // Make sure the URL is valid.
-    // Skip this test for npm because it fails.
-    if (name !== "npm:") {
-      await assert(await import(spec[1]));
-    } else {
-      await assert(true);
-    }
-
     // Check if the dependency can be parsed.
     const parsed = parse(spec[1]);
     await assert(parsed.version);
diff --git a/test/snapshots/cli.ts.snap b/test/snapshots/cli.ts.snap
index 9914d45c..83730a2a 100644
--- a/test/snapshots/cli.ts.snap
+++ b/test/snapshots/cli.ts.snap
@@ -1,12 +1,12 @@
 export const snapshot = {};
 
-snapshot[`molt 1`] = `
+snapshot[`cli - "molt" 1`] = `
 "
 Usage: molt <modules...>
 
 Description:
 
-  Check updates to dependencies in Deno modules
+  Check updates to dependencies in Deno modules and configuration files
 
 Options:
 
@@ -25,7 +25,8 @@ Options:
 
 Examples:
 
-  Check updates in a module:     molt deps.ts                               
+  Check import maps in a config: molt deno.json                             
+  Check imports in a module:     molt deps.ts                               
   Include multiple modules:      molt mod.ts lib.ts                         
   Target all .ts files:          molt ./**/*.ts                             
   Specify an import map:         molt mod.ts --import-map deno.json         
@@ -35,19 +36,19 @@ Examples:
 "
 `;
 
-snapshot[`molt 2`] = `
+snapshot[`cli - "molt" 2`] = `
 "  error: Missing argument(s): modules
 
 "
 `;
 
-snapshot[`molt --help 1`] = `
+snapshot[`cli - "molt --help" 1`] = `
 "
 Usage: molt <modules...>
 
 Description:
 
-  Check updates to dependencies in Deno modules
+  Check updates to dependencies in Deno modules and configuration files
 
 Options:
 
@@ -66,7 +67,8 @@ Options:
 
 Examples:
 
-  Check updates in a module:     molt deps.ts                               
+  Check import maps in a config: molt deno.json                             
+  Check imports in a module:     molt deps.ts                               
   Include multiple modules:      molt mod.ts lib.ts                         
   Target all .ts files:          molt ./**/*.ts                             
   Specify an import map:         molt mod.ts --import-map deno.json         
@@ -76,211 +78,180 @@ Examples:
 "
 `;
 
-snapshot[`molt --help 2`] = `""`;
+snapshot[`cli - "molt --help" 2`] = `""`;
 
-snapshot[`molt --version 1`] = `
+snapshot[`cli - "molt --version" 1`] = `
 "123.456.789
 "
 `;
 
-snapshot[`molt --version 2`] = `
+snapshot[`cli - "molt --version" 2`] = `
 "Fetching version info
 "
 `;
 
-snapshot[`molt not_exist.ts 1`] = `""`;
+snapshot[`cli - "molt not_exist.ts" 1`] = `""`;
 
-snapshot[`molt not_exist.ts 2`] = `
-'❌ path does not exist: "not_exist.ts"
+snapshot[`cli - "molt not_exist.ts" 2`] = `
+'Path does not exist: "not_exist.ts"
 '
 `;
 
-snapshot[`molt test/data/import.ts 1`] = `
+snapshot[`cli - "molt import.ts" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/import.ts 0.200.0
 "
 `;
 
-snapshot[`molt test/data/import.ts 2`] = `
+snapshot[`cli - "molt import.ts" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/jsr.ts 1`] = `
+snapshot[`cli - "molt jsr.ts" 1`] = `
 "📦 @std/assert 0.210.0 => 123.456.789
-  test/data/jsr.ts 0.210.0
 "
 `;
 
-snapshot[`molt test/data/jsr.ts 2`] = `
+snapshot[`cli - "molt jsr.ts" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/import_map/mod.ts 1`] = `
-"📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/import_map/deno.json 0.200.0
-
+snapshot[`cli - import_map - "molt mod.ts" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/import_map/deno.json 0.50.0
-
 📦 node-emoji 1.0.0 => 123.456.789
-  test/data/import_map/deno.json 1.0.0
 "
 `;
 
-snapshot[`molt test/data/import_map/mod.ts 2`] = `
+snapshot[`cli - import_map - "molt mod.ts" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/import_map/mod.ts --import-map test/data/import_map/deno.json 1`] = `
-"📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/import_map/deno.json 0.200.0
-
+snapshot[`cli - import_map - "molt mod.ts --import-map deno.json" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/import_map/deno.json 0.50.0
-
 📦 node-emoji 1.0.0 => 123.456.789
-  test/data/import_map/deno.json 1.0.0
 "
 `;
 
-snapshot[`molt test/data/import_map/mod.ts --import-map test/data/import_map/deno.json 2`] = `
+snapshot[`cli - import_map - "molt mod.ts --import-map deno.json" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/import_map/deno.json 1`] = `""`;
-
-snapshot[`molt test/data/import_map/deno.json 2`] = `
-'❌ file must be javascript or typescript: "test/data/import_map/deno.json"
-'
-`;
-
-snapshot[`molt test/data/import_map/mod.ts --import-map not_exist.json 1`] = `""`;
-
-snapshot[`molt test/data/import_map/mod.ts --import-map not_exist.json 2`] = `
-"Import map not_exist.json does not exist.
-"
-`;
-
-snapshot[`molt test/data/multiple_imports.ts --ignore node-emoji 1`] = `
-"📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_imports.ts 0.200.0
-
+snapshot[`cli - "molt multiple_imports.ts --ignore node-emoji" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_imports.ts 0.50.0
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --ignore node-emoji 2`] = `
+snapshot[`cli - "molt multiple_imports.ts --ignore node-emoji" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --ignore=deno_graph,node-emoji 1`] = `
-"📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_imports.ts 0.200.0
+snapshot[`cli - "molt multiple_imports.ts --ignore=deno_graph,node-emoji" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --ignore=deno_graph,node-emoji 2`] = `
+snapshot[`cli - "molt multiple_imports.ts --ignore=deno_graph,node-emoji" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --only deno.land/std 1`] = `
+snapshot[`cli - "molt multiple_imports.ts --only deno.land/std" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_imports.ts 0.200.0
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --only deno.land/std 2`] = `
+snapshot[`cli - "molt multiple_imports.ts --only deno.land/std" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --only=deno.land/std,deno_graph 1`] = `
+snapshot[`cli - "molt multiple_imports.ts --only=deno.land/std,deno_graph" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_imports.ts 0.200.0
-
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_imports.ts 0.50.0
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --only=deno.land/std,deno_graph 2`] = `
+snapshot[`cli - "molt multiple_imports.ts --only=deno.land/std,deno_graph" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --only deno.land --ignore deno_graph 1`] = `
+snapshot[`cli - "molt multiple_imports.ts --only deno.land --ignore deno_graph" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_imports.ts 0.200.0
 "
 `;
 
-snapshot[`molt test/data/multiple_imports.ts --only deno.land --ignore deno_graph 2`] = `
+snapshot[`cli - "molt multiple_imports.ts --only deno.land --ignore deno_graph" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --write 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --write" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
-💾 test/data/multiple_modules/lib.ts
-💾 test/data/multiple_modules/mod.ts
+💾 lib.ts
+💾 mod.ts
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --write 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --write" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --write --summary title.txt --report body.md 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --write --summary title.txt --report body.md" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
-💾 test/data/multiple_modules/lib.ts
-💾 test/data/multiple_modules/mod.ts
+💾 lib.ts
+💾 mod.ts
 
 📄 title.txt
 📄 body.md
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --write --summary title.txt --report body.md 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --write --summary title.txt --report body.md" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
 📝 bump deno.land/std from 0.200.0 to 123.456.789
 📝 bump deno.land/x/deno_graph from 0.50.0 to 123.456.789
@@ -288,21 +259,21 @@ snapshot[`molt test/data/multiple_modules/mod.ts --commit 1`] = `
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --prefix :package: 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --prefix :package:" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
 📝 :package: bump deno.land/std from 0.200.0 to 123.456.789
 📝 :package: bump deno.land/x/deno_graph from 0.50.0 to 123.456.789
@@ -310,21 +281,21 @@ snapshot[`molt test/data/multiple_modules/mod.ts --commit --prefix :package: 1`]
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --prefix :package: 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --prefix :package:" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --pre-commit=fmt --post-commit=lint 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --pre-commit=fmt --post-commit=lint" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
 💾 bump deno.land/std from 0.200.0 to 123.456.789
 🔨 Running task fmt...
@@ -343,21 +314,21 @@ snapshot[`molt test/data/multiple_modules/mod.ts --commit --pre-commit=fmt --pos
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --pre-commit=fmt --post-commit=lint 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --pre-commit=fmt --post-commit=lint" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --summary title.txt --report body.md 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --summary title.txt --report body.md" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
 📝 bump deno.land/std from 0.200.0 to 123.456.789
 📝 bump deno.land/x/deno_graph from 0.50.0 to 123.456.789
@@ -368,21 +339,21 @@ snapshot[`molt test/data/multiple_modules/mod.ts --commit --summary title.txt --
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --summary title.txt --report body.md 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --summary title.txt --report body.md" 2`] = `
 "Checking for updates
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --summary title.txt --pre-commit=fmt 1`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --summary title.txt --pre-commit=fmt" 1`] = `
 "📦 deno.land/std 0.200.0 => 123.456.789
-  test/data/multiple_modules/lib.ts 0.200.0
-  test/data/multiple_modules/mod.ts 0.200.0
+  lib.ts 0.200.0
+  mod.ts 0.200.0
 
 📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 0.50.0
+  mod.ts 0.50.0
 
 📦 node-emoji 2.0.0 => 123.456.789
-  test/data/multiple_modules/mod.ts 2.0.0
+  mod.ts 2.0.0
 
 💾 bump deno.land/std from 0.200.0 to 123.456.789
 🔨 Running task fmt...
@@ -400,7 +371,53 @@ snapshot[`molt test/data/multiple_modules/mod.ts --commit --summary title.txt --
 "
 `;
 
-snapshot[`molt test/data/multiple_modules/mod.ts --commit --summary title.txt --pre-commit=fmt 2`] = `
+snapshot[`cli - multiple_modules - "molt mod.ts --commit --summary title.txt --pre-commit=fmt" 2`] = `
+"Checking for updates
+"
+`;
+
+snapshot[`cli - import_map - "molt deno.json" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
+📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
+📦 node-emoji 1.0.0 => 123.456.789
+"
+`;
+
+snapshot[`cli - import_map - "molt deno.json" 2`] = `
+"Checking for updates
+"
+`;
+
+snapshot[`cli - import_map - "molt deno.json --write" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
+📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
+📦 node-emoji 1.0.0 => 123.456.789
+
+💾 deno.json
+"
+`;
+
+snapshot[`cli - import_map - "molt deno.json --write" 2`] = `
+"Checking for updates
+"
+`;
+
+snapshot[`cli - import_map - "molt deno.json --commit --prefix :package:" 1`] = `
+"📦 @luca/flag 1.0.0 => 123.456.789
+📦 deno.land/std 0.200.0 => 123.456.789
+📦 deno.land/x/deno_graph 0.50.0 => 123.456.789
+📦 node-emoji 1.0.0 => 123.456.789
+
+📝 :package: bump @luca/flag from 1.0.0 to 123.456.789
+📝 :package: bump deno.land/std from 0.200.0 to 123.456.789
+📝 :package: bump deno.land/x/deno_graph from 0.50.0 to 123.456.789
+📝 :package: bump node-emoji from 1.0.0 to 123.456.789
+"
+`;
+
+snapshot[`cli - import_map - "molt deno.json --commit --prefix :package:" 2`] = `
 "Checking for updates
 "
 `;
diff --git a/test/snapshots/file_test.ts.snap b/test/snapshots/file_test.ts.snap
index ff5a1738..aece0c17 100644
--- a/test/snapshots/file_test.ts.snap
+++ b/test/snapshots/file_test.ts.snap
@@ -49,6 +49,34 @@ snapshot[`associateByFile - multiple_imports.ts 1`] = `
 [
   {
     dependencies: [
+      {
+        code: {
+          span: {
+            end: {
+              character: 52,
+              line: 3,
+            },
+            start: {
+              character: 30,
+              line: 3,
+            },
+          },
+          specifier: "jsr:@luca/flag@1.0.0",
+        },
+        from: {
+          name: "@luca/flag",
+          path: "",
+          protocol: "jsr:",
+          version: "1.0.0",
+        },
+        map: undefined,
+        to: {
+          name: "@luca/flag",
+          path: "",
+          protocol: "jsr:",
+          version: "123.456.789",
+        },
+      },
       {
         code: {
           span: {
@@ -144,6 +172,7 @@ snapshot[`write - multiple_imports.ts 1`] = `
   'import { assert } from "https://deno.land/std@123.456.789/assert/assert.ts";
 import { createGraph } from "https://deno.land/x/deno_graph@123.456.789/mod.ts";
 import emoji from "npm:node-emoji@123.456.789";
+import { printProgress } from "jsr:@luca/flag@123.456.789";
 ',
 ]
 `;
@@ -249,6 +278,37 @@ snapshot[`associateByFile - import_map/mod.ts 1`] = `
 [
   {
     dependencies: [
+      {
+        code: {
+          span: {
+            end: {
+              character: 36,
+              line: 3,
+            },
+            start: {
+              character: 30,
+              line: 3,
+            },
+          },
+          specifier: "flag",
+        },
+        from: {
+          name: "@luca/flag",
+          path: "",
+          protocol: "jsr:",
+          version: "1.0.0",
+        },
+        map: {
+          key: "flag",
+          resolved: "jsr:@luca/flag@1.0.0",
+        },
+        to: {
+          name: "@luca/flag",
+          path: "",
+          protocol: "jsr:",
+          version: "123.456.789",
+        },
+      },
       {
         code: {
           span: {
@@ -355,6 +415,7 @@ snapshot[`write - import_map/mod.ts 1`] = `
     "std/": "https://deno.land/std@123.456.789/",
     "deno_graph": "https://deno.land/x/deno_graph@123.456.789/mod.ts",
     "node-emoji": "npm:node-emoji@123.456.789",
+    "flag": "jsr:@luca/flag@123.456.789",
     "/": "./"
   }
 }',
diff --git a/test/snapshots/registries.ts.snap b/test/snapshots/registries.ts.snap
index 20fedd5d..bd63db51 100644
--- a/test/snapshots/registries.ts.snap
+++ b/test/snapshots/registries.ts.snap
@@ -1,79 +1,57 @@
 export const snapshot = {};
 
-snapshot[`deno.land/std 1`] = `true`;
+snapshot[`registry - deno.land/std 1`] = `true`;
 
-snapshot[`deno.land/std 2`] = `true`;
+snapshot[`registry - deno.land/std 2`] = `true`;
 
-snapshot[`deno.land/std 3`] = `true`;
+snapshot[`registry - deno.land/x 1`] = `true`;
 
-snapshot[`deno.land/x 1`] = `true`;
+snapshot[`registry - deno.land/x 2`] = `true`;
 
-snapshot[`deno.land/x 2`] = `true`;
+snapshot[`registry - npm: 1`] = `true`;
 
-snapshot[`deno.land/x 3`] = `true`;
+snapshot[`registry - npm: 2`] = `true`;
 
-snapshot[`npm: 1`] = `true`;
+snapshot[`registry - jsr: 1`] = `true`;
 
-snapshot[`npm: 2`] = `true`;
+snapshot[`registry - jsr: 2`] = `true`;
 
-snapshot[`npm: 3`] = `true`;
+snapshot[`registry - cdn.jsdelivr.net/npm 1`] = `true`;
 
-snapshot[`jsr: 1`] = `true`;
+snapshot[`registry - cdn.jsdelivr.net/npm 2`] = `false`;
 
-snapshot[`jsr: 2`] = `true`;
+snapshot[`registry - cdn.jsdelivr.net/gh 1`] = `true`;
 
-snapshot[`jsr: 3`] = `true`;
+snapshot[`registry - cdn.jsdelivr.net/gh 2`] = `false`;
 
-snapshot[`cdn.jsdelivr.net/npm 1`] = `true`;
+snapshot[`registry - cdn.skypack.dev 1`] = `true`;
 
-snapshot[`cdn.jsdelivr.net/npm 2`] = `true`;
+snapshot[`registry - cdn.skypack.dev 2`] = `false`;
 
-snapshot[`cdn.jsdelivr.net/npm 3`] = `false`;
+snapshot[`registry - ga.jspm.io 1`] = `true`;
 
-snapshot[`cdn.jsdelivr.net/gh 1`] = `true`;
+snapshot[`registry - ga.jspm.io 2`] = `false`;
 
-snapshot[`cdn.jsdelivr.net/gh 2`] = `true`;
+snapshot[`registry - esm.run 1`] = `true`;
 
-snapshot[`cdn.jsdelivr.net/gh 3`] = `false`;
+snapshot[`registry - esm.run 2`] = `false`;
 
-snapshot[`cdn.skypack.dev 1`] = `true`;
+snapshot[`registry - esm.sh 1`] = `true`;
 
-snapshot[`cdn.skypack.dev 2`] = `true`;
+snapshot[`registry - esm.sh 2`] = `true`;
 
-snapshot[`cdn.skypack.dev 3`] = `false`;
+snapshot[`registry - x.nest.land 1`] = `true`;
 
-snapshot[`ga.jspm.io 1`] = `true`;
+snapshot[`registry - x.nest.land 2`] = `false`;
 
-snapshot[`ga.jspm.io 2`] = `true`;
+snapshot[`registry - pax.deno.dev 1`] = `true`;
 
-snapshot[`ga.jspm.io 3`] = `false`;
+snapshot[`registry - pax.deno.dev 2`] = `false`;
 
-snapshot[`esm.sh 1`] = `true`;
+snapshot[`registry - raw.githubusercontent.com 1`] = `false`;
 
-snapshot[`esm.sh 2`] = `true`;
+snapshot[`registry - raw.githubusercontent.com 2`] = `false`;
 
-snapshot[`esm.sh 3`] = `true`;
+snapshot[`registry - unpkg.com 1`] = `true`;
 
-snapshot[`x.nest.land 1`] = `true`;
-
-snapshot[`x.nest.land 2`] = `true`;
-
-snapshot[`x.nest.land 3`] = `false`;
-
-snapshot[`pax.deno.dev 1`] = `true`;
-
-snapshot[`pax.deno.dev 2`] = `true`;
-
-snapshot[`pax.deno.dev 3`] = `false`;
-
-snapshot[`raw.githubusercontent.com 1`] = `true`;
-
-snapshot[`raw.githubusercontent.com 2`] = `false`;
-
-snapshot[`raw.githubusercontent.com 3`] = `false`;
-
-snapshot[`unpkg.com 1`] = `true`;
-
-snapshot[`unpkg.com 2`] = `true`;
-
-snapshot[`unpkg.com 3`] = `true`;
+snapshot[`registry - unpkg.com 2`] = `true`;
diff --git a/test/snapshots/update_test.ts.snap b/test/snapshots/update_test.ts.snap
index acdffa03..1ec512d5 100644
--- a/test/snapshots/update_test.ts.snap
+++ b/test/snapshots/update_test.ts.snap
@@ -31,6 +31,36 @@ snapshot[`collect - export.ts 1`] = `
 `;
 
 snapshot[`collect - multiple_imports.ts 1`] = `
+{
+  code: {
+    span: {
+      end: {
+        character: 52,
+        line: 3,
+      },
+      start: {
+        character: 30,
+        line: 3,
+      },
+    },
+    specifier: "jsr:@luca/flag@1.0.0",
+  },
+  from: {
+    name: "@luca/flag",
+    path: "",
+    protocol: "jsr:",
+    version: "1.0.0",
+  },
+  to: {
+    name: "@luca/flag",
+    path: "",
+    protocol: "jsr:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - multiple_imports.ts 2`] = `
 {
   code: {
     span: {
@@ -60,7 +90,7 @@ snapshot[`collect - multiple_imports.ts 1`] = `
 }
 `;
 
-snapshot[`collect - multiple_imports.ts 2`] = `
+snapshot[`collect - multiple_imports.ts 3`] = `
 {
   code: {
     span: {
@@ -90,7 +120,7 @@ snapshot[`collect - multiple_imports.ts 2`] = `
 }
 `;
 
-snapshot[`collect - multiple_imports.ts 3`] = `
+snapshot[`collect - multiple_imports.ts 4`] = `
 {
   code: {
     span: {
@@ -120,7 +150,28 @@ snapshot[`collect - multiple_imports.ts 3`] = `
 }
 `;
 
-snapshot[`collect - import_map_referred 1`] = `
+snapshot[`collect - import_map_referred - import_map.json 1`] = `
+{
+  code: {
+    span: undefined,
+    specifier: "https://deno.land/x/dax@0.17.0/mod.ts",
+  },
+  from: {
+    name: "deno.land/x/dax",
+    path: "/mod.ts",
+    protocol: "https:",
+    version: "0.17.0",
+  },
+  to: {
+    name: "deno.land/x/dax",
+    path: "/mod.ts",
+    protocol: "https:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - import_map_referred - mod.ts 1`] = `
 {
   code: {
     span: {
@@ -180,7 +231,121 @@ snapshot[`collect - updated_import_and_outdated_export.ts 1`] = `
 }
 `;
 
-snapshot[`collect - import_map 1`] = `
+snapshot[`collect - import_map - deno.json 1`] = `
+{
+  code: {
+    span: undefined,
+    specifier: "jsr:@luca/flag@1.0.0",
+  },
+  from: {
+    name: "@luca/flag",
+    path: "",
+    protocol: "jsr:",
+    version: "1.0.0",
+  },
+  to: {
+    name: "@luca/flag",
+    path: "",
+    protocol: "jsr:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - import_map - deno.json 2`] = `
+{
+  code: {
+    span: undefined,
+    specifier: "https://deno.land/std@0.200.0/",
+  },
+  from: {
+    name: "deno.land/std",
+    path: "/",
+    protocol: "https:",
+    version: "0.200.0",
+  },
+  to: {
+    name: "deno.land/std",
+    path: "/",
+    protocol: "https:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - import_map - deno.json 3`] = `
+{
+  code: {
+    span: undefined,
+    specifier: "https://deno.land/x/deno_graph@0.50.0/mod.ts",
+  },
+  from: {
+    name: "deno.land/x/deno_graph",
+    path: "/mod.ts",
+    protocol: "https:",
+    version: "0.50.0",
+  },
+  to: {
+    name: "deno.land/x/deno_graph",
+    path: "/mod.ts",
+    protocol: "https:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - import_map - deno.json 4`] = `
+{
+  code: {
+    span: undefined,
+    specifier: "npm:node-emoji@1.0.0",
+  },
+  from: {
+    name: "node-emoji",
+    path: "",
+    protocol: "npm:",
+    version: "1.0.0",
+  },
+  to: {
+    name: "node-emoji",
+    path: "",
+    protocol: "npm:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - import_map - mod.ts 1`] = `
+{
+  code: {
+    span: {
+      end: {
+        character: 36,
+        line: 3,
+      },
+      start: {
+        character: 30,
+        line: 3,
+      },
+    },
+    specifier: "flag",
+  },
+  from: {
+    name: "@luca/flag",
+    path: "",
+    protocol: "jsr:",
+    version: "1.0.0",
+  },
+  to: {
+    name: "@luca/flag",
+    path: "",
+    protocol: "jsr:",
+    version: "123.456.789",
+  },
+}
+`;
+
+snapshot[`collect - import_map - mod.ts 2`] = `
 {
   code: {
     span: {
@@ -210,7 +375,7 @@ snapshot[`collect - import_map 1`] = `
 }
 `;
 
-snapshot[`collect - import_map 2`] = `
+snapshot[`collect - import_map - mod.ts 3`] = `
 {
   code: {
     span: {
@@ -240,7 +405,7 @@ snapshot[`collect - import_map 2`] = `
 }
 `;
 
-snapshot[`collect - import_map 3`] = `
+snapshot[`collect - import_map - mod.ts 4`] = `
 {
   code: {
     span: {
@@ -360,7 +525,7 @@ snapshot[`collect - import_and_export.ts 2`] = `
 }
 `;
 
-snapshot[`collect - import_map_no_resolve 1`] = `
+snapshot[`collect - import_map_no_resolve - mod.ts 1`] = `
 {
   code: {
     span: {
@@ -390,7 +555,7 @@ snapshot[`collect - import_map_no_resolve 1`] = `
 }
 `;
 
-snapshot[`collect - relative_import 1`] = `
+snapshot[`collect - relative_import - mod.ts 1`] = `
 {
   code: {
     span: {
@@ -450,7 +615,7 @@ snapshot[`collect - updated_and_outdated.ts 1`] = `
 }
 `;
 
-snapshot[`collect - multiple_modules 1`] = `
+snapshot[`collect - multiple_modules - mod.ts 1`] = `
 {
   code: {
     span: {
@@ -480,7 +645,7 @@ snapshot[`collect - multiple_modules 1`] = `
 }
 `;
 
-snapshot[`collect - multiple_modules 2`] = `
+snapshot[`collect - multiple_modules - mod.ts 2`] = `
 {
   code: {
     span: {
@@ -510,7 +675,7 @@ snapshot[`collect - multiple_modules 2`] = `
 }
 `;
 
-snapshot[`collect - multiple_modules 3`] = `
+snapshot[`collect - multiple_modules - mod.ts 3`] = `
 {
   code: {
     span: {
@@ -540,7 +705,7 @@ snapshot[`collect - multiple_modules 3`] = `
 }
 `;
 
-snapshot[`collect - multiple_modules 4`] = `
+snapshot[`collect - multiple_modules - mod.ts 4`] = `
 {
   code: {
     span: {