diff --git a/.gitignore b/.gitignore
index 5497eeb..3de77e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,5 +11,6 @@ pnpm-lock.yaml
 
 # Test run-time fixtures
 test-collection
+test-collection-b
 test-theme
 .shopify
diff --git a/package-lock.json b/package-lock.json
index 053c568..cebce07 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "plugin-devkit",
-  "version": "1.0.3",
+  "version": "1.0.4",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "plugin-devkit",
-      "version": "1.0.3",
+      "version": "1.0.4",
       "license": "MIT",
       "dependencies": {
         "@oclif/core": "^4",
diff --git a/package.json b/package.json
index 4f0e5b6..68c63a6 100644
--- a/package.json
+++ b/package.json
@@ -20,6 +20,7 @@
     "build": "shx rm -rf dist && tsc -b",
     "watch": "tsc --watch",
     "lint": "eslint . --ext .ts",
+    "lint:fix": "eslint . --ext .ts --fix",
     "test": "mocha --forbid-only \"test/**/*.test.ts\"",
     "posttest": "npm run lint",
     "prepack": "oclif manifest && oclif readme",
diff --git a/src/commands/theme/component/clean.ts b/src/commands/theme/component/clean.ts
index 5477fda..dc1ca9c 100644
--- a/src/commands/theme/component/clean.ts
+++ b/src/commands/theme/component/clean.ts
@@ -11,11 +11,13 @@ import path from 'node:path'
 import Args from '../../../utilities/args.js'
 import BaseCommand from '../../../utilities/base-command.js'
 import { getManifest } from '../../../utilities/manifest.js'
-import { getThemeNodes } from '../../../utilities/nodes.js'
+import { getCollectionNodes, getThemeNodes } from '../../../utilities/nodes.js'
+import { LiquidNode } from '../../../utilities/types.js'
+import { isComponentRepo, isThemeRepo } from '../../../utilities/validate.js'
 
 export default class Clean extends BaseCommand {
   static override args = Args.getDefinitions([
-    Args.override(Args.THEME_DIR, { default: '.', required: false })
+    Args.override(Args.DEST_DIR, { default: '.', required: false })
   ])
 
   static override description = 'Remove unused component files in a theme'
@@ -29,21 +31,28 @@ export default class Clean extends BaseCommand {
   }
 
   public async run(): Promise<void> {
-    const themeDir = path.resolve(process.cwd(), this.args[Args.THEME_DIR])
+    const destinationDir = path.resolve(process.cwd(), this.args[Args.DEST_DIR])
 
-    const manifest = getManifest(path.join(themeDir, 'component.manifest.json'))
-    const themeNodes = await getThemeNodes(themeDir)
+    const manifest = getManifest(path.join(destinationDir, 'component.manifest.json'))
 
-    // Remove files that are not in the component map
-    for (const node of themeNodes) {
+    let destinationNodes: LiquidNode[]
+    if (isThemeRepo(destinationDir)) {
+      destinationNodes = await getThemeNodes(destinationDir)
+    } else if (isComponentRepo(destinationDir)) {
+      destinationNodes = await getCollectionNodes(destinationDir)
+    } else {
+      this.error('Warning: Destination directory does not appear to be a theme or component collection.')
+    }
+
+    // Remove files that are not in the component manifest
+    for (const node of destinationNodes) {
       if (node.type === 'snippet' || node.type === 'asset') {
         const collection = node.type === 'snippet' ? manifest.files.snippets : manifest.files.assets;
-        if (!collection[node.name]) {
-          const filePath = path.join(themeDir, node.themeFolder, node.name);
-          if (fs.existsSync(filePath)) {
-            fs.rmSync(filePath);
-          }
+        if (!collection[node.name] && fs.existsSync(node.file)) {
+          fs.rmSync(node.file);
         }
+      } else if (node.type === 'component' && !manifest.files.snippets[node.name] && fs.existsSync(node.file)) {
+        fs.rmSync(path.dirname(node.file), { recursive: true });
       }
     }
   }
diff --git a/src/commands/theme/component/copy.ts b/src/commands/theme/component/copy.ts
index 757bcac..4920b1c 100644
--- a/src/commands/theme/component/copy.ts
+++ b/src/commands/theme/component/copy.ts
@@ -13,12 +13,13 @@ import BaseCommand from '../../../utilities/base-command.js'
 import { copyFileIfChanged } from '../../../utilities/files.js';
 import Flags from '../../../utilities/flags.js'
 import { getManifest } from '../../../utilities/manifest.js'
-import { getCollectionNodes } from '../../../utilities/nodes.js'
+import { getCollectionNodes, getDuplicateFiles } from '../../../utilities/nodes.js'
 import { getNameFromPackageJson, getVersionFromPackageJson } from '../../../utilities/package-json.js'
+import { isComponentRepo, isThemeRepo } from '../../../utilities/validate.js'
 
 export default class Copy extends BaseCommand {
   static override args = Args.getDefinitions([
-    Args.THEME_DIR
+    Args.DEST_DIR
   ])
 
   static override description = 'Copy files from a component collection into a theme'
@@ -38,36 +39,70 @@ export default class Copy extends BaseCommand {
 
   public async run(): Promise<void> {
     const currentDir = process.cwd()
-    const hasPackageJson = fs.existsSync(path.join(currentDir, 'package.json'))
-    const hasComponentsDir = fs.existsSync(path.join(currentDir, 'components'))
 
-    if (!hasPackageJson || !hasComponentsDir) {
+    if (!isComponentRepo(currentDir)) {
       this.error('Warning: Current directory does not appear to be a component collection. Expected to find package.json and components directory.')
     }
 
-    const themeDir = path.resolve(currentDir, this.args[Args.THEME_DIR])
-    const collectionName = this.flags[Flags.COLLECTION_NAME] || getNameFromPackageJson(process.cwd())
-    const collectionVersion = this.flags[Flags.COLLECTION_VERSION] || getVersionFromPackageJson(process.cwd())
+    const destinationDir = path.resolve(currentDir, this.args[Args.DEST_DIR])
+    const sourceName = this.flags[Flags.COLLECTION_NAME] || getNameFromPackageJson(process.cwd())
+    const sourceVersion = this.flags[Flags.COLLECTION_VERSION] || getVersionFromPackageJson(process.cwd())
 
-    if (!fs.existsSync(path.join(themeDir, 'component.manifest.json'))) {
-      this.error('Error: component.manifest.json file not found in the theme directory. Run "shopify theme component map" to generate a component.manifest.json file.');
+    if (!fs.existsSync(path.join(destinationDir, 'component.manifest.json'))) {
+      this.error('Error: component.manifest.json file not found in the destination directory. Run "shopify theme component map" to generate a component.manifest.json file.');
     }
 
-    const manifest = getManifest(path.join(themeDir, 'component.manifest.json'))
+    const manifest = getManifest(path.join(destinationDir, 'component.manifest.json'))
     const componentNodes = await getCollectionNodes(currentDir)
 
-    if (manifest.collections[collectionName].version !== collectionVersion) {
-      this.error(`Version mismatch: Expected ${collectionVersion} but found ${manifest.collections[collectionName].version}. Run "shopify theme component map" to update the component.manifest.json file.`);
+    const duplicates = getDuplicateFiles(componentNodes);
+
+    if (duplicates.size > 0) {
+      const message: string[] = []
+      for (const [key, nodes] of duplicates) {
+        message.push(`Warning: Found duplicate files for ${key}:`)
+        for (const node of nodes) {
+          message.push(`  - ${node.file}`)
+        }
+      }
+
+      this.error(message.join('\n'))
+    }
+
+    if (manifest.collections[sourceName].version !== sourceVersion) {
+      this.error(`Version mismatch: Expected ${sourceVersion} but found ${manifest.collections[sourceName].version}. Run "shopify theme component map" to update the component.manifest.json file.`);
     }
 
     const copyManifestFiles = (fileType: 'assets' | 'snippets') => {
       for (const [fileName, fileCollection] of Object.entries(manifest.files[fileType])) {
-        if (fileCollection === collectionName) {
-          const node = componentNodes.find(node => node.name === fileName && node.themeFolder === fileType);
-          if (node) {
-            const src = node.file;
-            const dest = path.join(themeDir, fileType, fileName);
-            copyFileIfChanged(src, dest);
+        if (fileCollection !== sourceName) continue;
+
+        const node = componentNodes.find(node => node.name === fileName && node.themeFolder === fileType);
+
+        if (!node) continue;
+
+        if (isThemeRepo(destinationDir)) {
+          copyFileIfChanged(node.file, path.join(destinationDir, fileType, fileName));
+        } else if (isComponentRepo(destinationDir)) {
+          const dest = node.file.replace(currentDir, destinationDir)
+          copyFileIfChanged(node.file, dest);
+
+          if (node.type === 'component') {
+            // Copy setup and test folders if they exist
+            const setupSrcDir = path.join(path.dirname(node.file), 'setup');
+            const setupDestDir = path.join(path.dirname(dest), 'setup');
+            const testSrcDir = path.join(path.dirname(node.file), 'test');
+            const testDestDir = path.join(path.dirname(dest), 'test');
+
+            if (fs.existsSync(setupSrcDir)) {
+              fs.mkdirSync(setupDestDir, { recursive: true });
+              fs.cpSync(setupSrcDir, setupDestDir, { recursive: true });
+            }
+
+            if (fs.existsSync(testSrcDir)) {
+              fs.mkdirSync(testDestDir, { recursive: true });
+              fs.cpSync(testSrcDir, testDestDir, { recursive: true });
+            }
           }
         }
       }
diff --git a/src/commands/theme/component/install.ts b/src/commands/theme/component/install.ts
index f92ee2d..7feeed6 100644
--- a/src/commands/theme/component/install.ts
+++ b/src/commands/theme/component/install.ts
@@ -10,14 +10,15 @@
 import Args from '../../../utilities/args.js'
 import BaseCommand from '../../../utilities/base-command.js'
 import Flags from '../../../utilities/flags.js'
+import {isThemeRepo} from '../../../utilities/validate.js'
 import GenerateImportMap from '../generate/import-map.js'
 import Clean from './clean.js'
 import Copy from './copy.js'
-import Map from './map.js'
+import Manifest from './manifest.js'
 
 export default class Install extends BaseCommand {
   static override args = Args.getDefinitions([
-    Args.THEME_DIR,
+    Args.DEST_DIR,
     Args.COMPONENT_SELECTOR
   ])
 
@@ -39,9 +40,12 @@ export default class Install extends BaseCommand {
   }
 
   public async run(): Promise<void> {
-    await Map.run([this.args[Args.THEME_DIR]!])
-    await Copy.run([this.args[Args.THEME_DIR]!])
-    await Clean.run([this.args[Args.THEME_DIR]!])
-    await GenerateImportMap.run([this.args[Args.THEME_DIR]!, '--quiet'])
+    await Manifest.run([this.args[Args.DEST_DIR]!])
+    await Copy.run([this.args[Args.DEST_DIR]!])
+    await Clean.run([this.args[Args.DEST_DIR]!])
+
+    if (isThemeRepo(this.args[Args.DEST_DIR])) {
+      await GenerateImportMap.run([this.args[Args.DEST_DIR]!, '--quiet'])
+    }
   }
 }
diff --git a/src/commands/theme/component/manifest.ts b/src/commands/theme/component/manifest.ts
new file mode 100644
index 0000000..4dc3b30
--- /dev/null
+++ b/src/commands/theme/component/manifest.ts
@@ -0,0 +1,116 @@
+/**
+ * This command generates or updates a component.manifest.json file
+ *
+ * - Updates component files (assets and snippets) mapping
+ * - Updates component collection details
+ */
+
+import fs from 'node:fs'
+import path from 'node:path'
+
+import Args from '../../../utilities/args.js'
+import BaseCommand from '../../../utilities/base-command.js'
+import Flags from '../../../utilities/flags.js'
+import { getLastCommitHash } from '../../../utilities/git.js'
+import { ManifestOptions, generateManifestFile, getManifest } from '../../../utilities/manifest.js'
+import { getCollectionNodes, getDuplicateFiles, getThemeNodes } from '../../../utilities/nodes.js'
+import { sortObjectKeys } from '../../../utilities/objects.js'
+import { getNameFromPackageJson, getVersionFromPackageJson } from '../../../utilities/package-json.js'
+import { LiquidNode } from '../../../utilities/types.js'
+import { isComponentRepo, isThemeRepo } from '../../../utilities/validate.js'
+
+export default class Manifest extends BaseCommand {
+  static override args = Args.getDefinitions([
+    Args.DEST_DIR,
+    Args.COMPONENT_SELECTOR
+  ])
+
+  static override description = 'Generates or updates a component.manifest.json file with the component collection details and a file map'
+
+  static override examples = [
+    '<%= config.bin %> <%= command.id %> theme-directory',
+    '<%= config.bin %> <%= command.id %> theme-directory header',
+    '<%= config.bin %> <%= command.id %> theme-directory header,footer,navigation'
+  ]
+
+  static override flags = Flags.getDefinitions([
+    Flags.COLLECTION_NAME,
+    Flags.COLLECTION_VERSION,
+    Flags.IGNORE_CONFLICTS,
+    Flags.IGNORE_OVERRIDES
+  ])
+
+  protected override async init(): Promise<void> {
+    await super.init(Manifest)
+  }
+
+  public async run(): Promise<void> {
+    const sourceDir = process.cwd()
+
+    if (!isComponentRepo(sourceDir)) {
+      this.error('Warning: Current directory does not appear to be a component collection or theme repository. Expected to find package.json and components directory.')
+    }
+
+    const destinationDir = path.resolve(sourceDir, this.args[Args.DEST_DIR])
+    const sourceName = this.flags[Flags.COLLECTION_NAME] || getNameFromPackageJson(process.cwd())
+    const sourceVersion = this.flags[Flags.COLLECTION_VERSION] || getVersionFromPackageJson(process.cwd())
+    const ignoreConflicts = this.flags[Flags.IGNORE_CONFLICTS]
+    const ignoreOverrides = this.flags[Flags.IGNORE_OVERRIDES]
+    const componentSelector = this.args[Args.COMPONENT_SELECTOR]
+
+    const manifestPath = path.join(destinationDir, 'component.manifest.json')
+    const manifest = getManifest(manifestPath);
+
+    const options: ManifestOptions = {
+      componentSelector,
+      ignoreConflicts,
+      ignoreOverrides
+    }
+
+    const sourceNodes = await getCollectionNodes(sourceDir)
+
+    const duplicates = getDuplicateFiles(sourceNodes);
+
+    if (duplicates.size > 0) {
+      const message: string[] = []
+      for (const [key, nodes] of duplicates) {
+        message.push(`Warning: Found duplicate files for ${key}:`)
+        for (const node of nodes) {
+          message.push(`  - ${node.file}`)
+        }
+      }
+
+      this.error(message.join('\n'))
+    }
+
+    let destinationNodes: LiquidNode[]
+    let destinationName: string
+
+    if (isThemeRepo(destinationDir)) {
+      destinationNodes = await getThemeNodes(destinationDir)
+      destinationName = '@theme'
+    } else if (isComponentRepo(destinationDir)) {
+      destinationNodes = await getCollectionNodes(destinationDir)
+      destinationName = '@collection'
+    } else {
+      this.error('Warning: Destination directory does not appear to be a theme repository or component collection.')
+    }
+
+    const files = await generateManifestFile(
+      manifest.files,
+      destinationNodes,
+      destinationName,
+      sourceNodes,
+      sourceName,
+      options
+    )
+
+    manifest.files = sortObjectKeys(files)
+    manifest.collections[sourceName] = {
+      commit: getLastCommitHash(sourceDir),
+      version: sourceVersion
+    }
+
+    fs.writeFileSync(manifestPath, JSON.stringify(sortObjectKeys(manifest), null, 2))
+  }
+}
diff --git a/src/commands/theme/component/map.ts b/src/commands/theme/component/map.ts
deleted file mode 100644
index 51948b8..0000000
--- a/src/commands/theme/component/map.ts
+++ /dev/null
@@ -1,86 +0,0 @@
-/**
- * This command generates or updates a component.manifest.json file
- *
- * - Updates component files (assets and snippets) mapping
- * - Updates component collection details
- */
-
-import fs from 'node:fs'
-import path from 'node:path'
-
-import Args from '../../../utilities/args.js'
-import BaseCommand from '../../../utilities/base-command.js'
-import Flags from '../../../utilities/flags.js'
-import { getLastCommitHash } from '../../../utilities/git.js'
-import { ManifestOptions, generateManifestFiles, getManifest } from '../../../utilities/manifest.js'
-import { sortObjectKeys } from '../../../utilities/objects.js'
-import { getNameFromPackageJson, getVersionFromPackageJson } from '../../../utilities/package-json.js'
-
-export default class Manifest extends BaseCommand {
-  static override args = Args.getDefinitions([
-    Args.THEME_DIR,
-    Args.COMPONENT_SELECTOR
-  ])
-
-  static override description = 'Generates or updates a component.manifest.json file with the component collection details and a file map'
-
-  static override examples = [
-    '<%= config.bin %> <%= command.id %> theme-directory',
-    '<%= config.bin %> <%= command.id %> theme-directory header',
-    '<%= config.bin %> <%= command.id %> theme-directory header,footer,navigation'
-  ]
-
-  static override flags = Flags.getDefinitions([
-    Flags.COLLECTION_NAME,
-    Flags.COLLECTION_VERSION,
-    Flags.IGNORE_CONFLICTS,
-    Flags.IGNORE_OVERRIDES
-  ])
-
-  protected override async init(): Promise<void> {
-    await super.init(Manifest)
-  }
-
-  public async run(): Promise<void> {
-    const currentDir = process.cwd()
-    const hasPackageJson = fs.existsSync(path.join(currentDir, 'package.json'))
-    const hasComponentsDir = fs.existsSync(path.join(currentDir, 'components'))
-
-    if (!hasPackageJson || !hasComponentsDir) {
-      this.error('Warning: Current directory does not appear to be a component collection. Expected to find package.json and components directory.')
-    }
-
-    const themeDir = path.resolve(currentDir, this.args[Args.THEME_DIR])
-    const collectionDir = currentDir
-    const collectionName = this.flags[Flags.COLLECTION_NAME] || getNameFromPackageJson(process.cwd())
-    const collectionVersion = this.flags[Flags.COLLECTION_VERSION] || getVersionFromPackageJson(process.cwd())
-    const ignoreConflicts = this.flags[Flags.IGNORE_CONFLICTS]
-    const ignoreOverrides = this.flags[Flags.IGNORE_OVERRIDES]
-    const componentSelector = this.args[Args.COMPONENT_SELECTOR]
-
-    const manifestPath = path.join(themeDir, 'component.manifest.json')
-    const manifest = getManifest(manifestPath);
-
-    const options: ManifestOptions = {
-      componentSelector,
-      ignoreConflicts,
-      ignoreOverrides
-    }
-
-    const files = await generateManifestFiles(
-      manifest.files,
-      themeDir,
-      collectionDir,
-      collectionName,
-      options
-    )
-
-    manifest.files = sortObjectKeys(files)
-    manifest.collections[collectionName] = {
-      commit: getLastCommitHash(collectionDir),
-      version: collectionVersion
-    }
-
-    fs.writeFileSync(manifestPath, JSON.stringify(sortObjectKeys(manifest), null, 2))
-  }
-}
diff --git a/src/commands/theme/generate/import-map.ts b/src/commands/theme/generate/import-map.ts
index bf60f66..d2a6f0c 100644
--- a/src/commands/theme/generate/import-map.ts
+++ b/src/commands/theme/generate/import-map.ts
@@ -14,13 +14,13 @@ import BaseCommand from '../../../utilities/base-command.js'
 import Flags from '../../../utilities/flags.js'
 export default class GenerateImportMap extends BaseCommand {
   static override args = Args.getDefinitions([
-    Args.override(Args.THEME_DIR, { default: '.', required: false })
+    Args.override(Args.DEST_DIR, { default: '.', required: false })
   ])
 
   static description = 'Generate an import map for JavaScript files in the assets directory'
 
   async run() {
-    const themeDir = path.resolve(process.cwd(), this.args[Args.THEME_DIR])
+    const themeDir = path.resolve(process.cwd(), this.args[Args.DEST_DIR])
     const assetsDir = path.join(themeDir, 'assets')
     const snippetsDir = path.join(themeDir, 'snippets')
 
diff --git a/src/utilities/args.ts b/src/utilities/args.ts
index c944466..d3bc446 100644
--- a/src/utilities/args.ts
+++ b/src/utilities/args.ts
@@ -1,16 +1,15 @@
 import {Args as OclifArgs} from '@oclif/core'
 import { ArgInput } from '@oclif/core/interfaces'
 import {glob} from 'glob'
-import fs from 'node:fs'
-import path from 'node:path'
 
 import logger from './logger.js'
+import {isComponentRepo, isThemeRepo} from './validate.js'
 
 export default class Args {
   [key: string]: any // eslint-disable-line @typescript-eslint/no-explicit-any
   static readonly COMPONENT_SELECTOR = 'componentSelector'
+  static readonly DEST_DIR = 'destDir'
   static readonly THEME_DIR = 'themeDir'
-
   constructor(args: Record<string, ArgInput<object>>) {
     Object.assign(this, args)
   }
@@ -62,20 +61,27 @@ export const argDefinitions: Record<string, any> = {
     required: false
   }),
 
+  [Args.DEST_DIR]: OclifArgs.string({
+    description: 'path to component install directory', 
+    async parse(input: string): Promise<string> {
+      logger.debug(`Parsing destination directory argument '${input}'`)
+
+      if (!isComponentRepo(input) && !isThemeRepo(input)) {
+        logger.error(new Error(`The provided path ${input} does not appear to be a valid component collection or theme repository.`), {exit: 1})
+      }
+
+      logger.debug(`Destination directory ${input} appears to be valid`)
+      return input
+    },
+    required: true
+  }),
+
   [Args.THEME_DIR]: OclifArgs.string({
     description: 'path to theme directory', 
     async parse(input: string): Promise<string> {
       logger.debug(`Parsing theme directory argument '${input}'`)
-      const requiredFolders = ['layout', 'templates', 'config']
-      let isThemeDirectory = true
-
-      for (const folder of requiredFolders) {
-        if (!fs.existsSync(path.join(input, folder))) {
-          isThemeDirectory = false
-        }
-      }
 
-      if (!isThemeDirectory) {
+      if (!isThemeRepo(input)) {
         logger.error(new Error(`The provided path ${input} does not appear to contain valid theme files.`), {exit: 1})
       }
 
diff --git a/src/utilities/manifest.ts b/src/utilities/manifest.ts
index 07e262e..d222d5a 100644
--- a/src/utilities/manifest.ts
+++ b/src/utilities/manifest.ts
@@ -1,7 +1,6 @@
 import * as fs from 'node:fs'
 
 import logger from './logger.js'
-import { getCollectionNodes, getThemeNodes } from './nodes.js'
 import { LiquidNode, Manifest } from './types.js'
 
 export function getManifest(path: string): Manifest {
@@ -25,40 +24,39 @@ export interface ManifestOptions {
 }
 
 // eslint-disable-next-line max-params
-export async function generateManifestFiles(
+export async function generateManifestFile(
   oldFilesMap: Manifest['files'],
-  themeDir: string, 
-  collectionDir: string,
-  collectionName: string,
+  destinationNodes: LiquidNode[],
+  destinationName: string,
+  sourceNodes: LiquidNode[],
+  sourceName: string,
   options: ManifestOptions
 ): Promise<Manifest['files']> {
-  const collectionNodes = await getCollectionNodes(collectionDir)
-  const themeNodes = await getThemeNodes(themeDir)
-  const entryPointNodes = themeNodes.filter(node => node.type === 'entry')
+  const entryPointNodes = destinationNodes.filter(node => node.type === 'component' || node.type === 'entry')
 
   const newFilesMap: Manifest['files'] = {
     assets: {},
     snippets: {}
   }
 
-  // Track collection nodes that are selected or children of selected components
-  const selectedCollectionNodes = new Set<LiquidNode>()
+  // Track source nodes that are selected or children of selected source nodes
+  const selectedSourceNodes = new Set<LiquidNode>()
   
   function addNodeAndChildren(nodeName: string, visited = new Set<string>()) {
     if (visited.has(nodeName)) return // Prevent infinite recursion
     visited.add(nodeName)
 
-    const node = collectionNodes.find(n => n.name === nodeName)
+    const node = sourceNodes.find(n => n.name === nodeName)
     if (!node) return
     
-    selectedCollectionNodes.add(node)
+    selectedSourceNodes.add(node)
 
     // Add all child snippets and recursively check their children
     if (node.snippets) {
       for (const snippet of node.snippets) {
-        const snippetNode = collectionNodes.find(n => n.name === snippet)
+        const snippetNode = sourceNodes.find(n => n.name === snippet)
         if (snippetNode) {
-          selectedCollectionNodes.add(snippetNode)
+          selectedSourceNodes.add(snippetNode)
           addNodeAndChildren(snippet, visited)
         }
       }
@@ -67,9 +65,9 @@ export async function generateManifestFiles(
     // Add all child assets and recursively check their dependencies
     if (node.assets) {
       for (const asset of node.assets) {
-        const assetNode = collectionNodes.find(n => n.name === asset)
+        const assetNode = sourceNodes.find(n => n.name === asset)
         if (assetNode) {
-          selectedCollectionNodes.add(assetNode)
+          selectedSourceNodes.add(assetNode)
           addNodeAndChildren(asset, visited)
         }
       }
@@ -80,36 +78,36 @@ export async function generateManifestFiles(
     const selectedComponents = options.componentSelector.split(',')
     for (const component of selectedComponents) addNodeAndChildren(`${component}.liquid`)
     // Throw error if no components were matched
-    if (selectedCollectionNodes.size === 0) {
+    if (selectedSourceNodes.size === 0) {
       logger.error(`No components found matching selector: ${options.componentSelector}`)
     }
   }
 
-  for (const node of themeNodes) {
-    // Add theme nodes not present in the old import map
+  for (const node of destinationNodes) {
+    // Add destination nodes not present in the old import map
     // They have been added manually by the user since the last time the import map was generated
-    if ((node.type === 'snippet' || node.type === 'asset') && !oldFilesMap[node.themeFolder]?.[node.name]) {
-        const collectionNode = collectionNodes.find(n => n.themeFolder === node.themeFolder && n.name === node.name)
+    if ((node.type === 'snippet' || node.type === 'asset' || node.type === 'component') && !oldFilesMap[node.themeFolder]?.[node.name]) {
+        const destinationNode = sourceNodes.find(n => n.themeFolder === node.themeFolder && n.name === node.name)
 
-        if (collectionNode) {
+        if (destinationNode) {
           if (options.ignoreConflicts) {
-            // If the user has passed the --ignore-conflicts flag, skip the node so it can be logged later as a component entry
+            // If the user has passed the --ignore-conflicts flag, skip the node so it can be logged later as a source entry
             continue;
           } else {
-            // If the node also exists in the collection, warn the user of the potential conflict but keep as a @theme entry
-            newFilesMap[node.themeFolder][node.name] = '@theme'
-            logger.log(`Conflict Warning: Pre-existing file ${node.themeFolder}/${node.name} without mapping conflicts with file in ${collectionName}. Keeping the theme file.`)
+            // If the node also exists in the source, warn the user of the potential conflict but keep as a destination entry
+            newFilesMap[node.themeFolder][node.name] = destinationName
+            logger.log(`Conflict Warning: Pre-existing file ${node.themeFolder}/${node.name} without mapping conflicts with file in ${sourceName}. Keeping the file from ${destinationName}.`)
           }
         } else {
-          // If the node does not exist in the collection, add it to the new import map as a @theme entry
-          newFilesMap[node.themeFolder][node.name] = '@theme'
+          // If the node does not exist in the source, add it to the new import map as a destination entry
+          newFilesMap[node.themeFolder][node.name] = destinationName
         }
       }
 
-    // Persist prexisting asset entries from @theme or other collections
+    // Persist prexisting asset entries from destination
     if (node.type === 'asset') {
       const oldImportMapValue = oldFilesMap[node.themeFolder]?.[node.name]
-      if (oldImportMapValue !== collectionName && typeof oldImportMapValue === 'string') {
+      if (oldImportMapValue !== sourceName && typeof oldImportMapValue === 'string') {
         newFilesMap[node.themeFolder][node.name] = oldImportMapValue
       }
     }
@@ -122,24 +120,24 @@ export async function generateManifestFiles(
     // If the new import map value is already defined, we don't need to add it again
     if (newImportMapValue !== undefined) return
 
-    if (oldImportMapValue !== collectionName && typeof oldImportMapValue === 'string') {
-      // If the import map value is not our collection but is defined
-      let node = themeNodes.find(node => node.themeFolder === themeFolder && node.name === name)
+    if (oldImportMapValue !== sourceName && typeof oldImportMapValue === 'string') {
+      // If the import map value is not in our source but is defined
+      let node = destinationNodes.find(node => node.themeFolder === themeFolder && node.name === name)
       if (node) {
-        const collectionNode = collectionNodes.find(node => node.themeFolder === themeFolder && node.name === name)
-        if (collectionNode) {
-          // If the node also exists in the collection, it's considered an override
+        const destinationNode = sourceNodes.find(node => node.themeFolder === themeFolder && node.name === name)
+        if (destinationNode) {
+          // If the destination node also exists in our source, it's considered an override
           if (options.ignoreOverrides) {
-            // If the user has passed the --ignore-overrides, set the new import map value to the collection name
-            newFilesMap[node.themeFolder][node.name] = collectionName
-            node = collectionNode
+            // If the user has passed the --ignore-overrides, set the new import map value to the source name
+            newFilesMap[node.themeFolder][node.name] = sourceName
+            node = destinationNode
           } else {
             // If the user has not passed the --ignore-overrides flag, keep the override
             newFilesMap[node.themeFolder][node.name] = oldImportMapValue
-            logger.log(`Override Warning: ${node.themeFolder}/${node.name} is being overridden by the collection ${collectionName}.`)
+            logger.log(`Override Warning: ${node.themeFolder}/${node.name} is being overridden by the collection ${sourceName}.`)
           }
         } else {
-          // If the node does not exist in the collection, add it to the new import map
+          // If the node does not exist in the source, add it to the new import map
           newFilesMap[node.themeFolder][node.name] = oldImportMapValue
         }
 
@@ -150,17 +148,17 @@ export async function generateManifestFiles(
           }
         }
       }
-    } else if (oldImportMapValue === collectionName || oldImportMapValue === undefined) {
+    } else if (oldImportMapValue === sourceName || oldImportMapValue === undefined) {
       // Skip if we have a component selector (not '*') and this node is not selected or a child of a selected component
-      if (options.componentSelector && options.componentSelector !== '*' && ![...selectedCollectionNodes].some(node => node.name === name)) {
+      if (options.componentSelector && options.componentSelector !== '*' && ![...selectedSourceNodes].some(node => node.name === name)) {
         return
       }
       
       // If the import map value is set our collection or undefined
-      const node = collectionNodes.find(node => node.themeFolder === themeFolder && node.name === name)
+      const node = sourceNodes.find(node => node.themeFolder === themeFolder && node.name === name)
       if (node) {
         // If the node exists in the collection, add it to the new import map
-        newFilesMap[node.themeFolder][node.name] = collectionName
+        newFilesMap[node.themeFolder][node.name] = sourceName
         if (node.assets.length > 0) {
           // If the node is a component, add its assets to the new import map
           for (const asset of node.assets) addFilesMapEntry('assets', asset)
@@ -178,8 +176,12 @@ export async function generateManifestFiles(
 
   // Build out the import map for the theme and collection
   for (const node of entryPointNodes) {
-    for (const snippet of node.snippets) {
-      addFilesMapEntry('snippets', snippet)
+    if (node.type === 'component') {
+      addFilesMapEntry('snippets', node.name)
+    } else if (node.type === 'entry') {
+      for (const snippet of node.snippets) {
+        addFilesMapEntry('snippets', snippet)
+      }
     }
   }
 
diff --git a/src/utilities/nodes.ts b/src/utilities/nodes.ts
index f0cf0f1..56e020a 100644
--- a/src/utilities/nodes.ts
+++ b/src/utilities/nodes.ts
@@ -65,7 +65,7 @@ export async function generateLiquidNode(file: string, type: LiquidNode['type'],
     assets = await getJsAssets(body)
   }
 
-  if (type === 'snippet') { 
+  if (type === 'snippet') {
     body = fs.readFileSync(file, 'utf8')
     assets = getJsImportsFromLiquid(body)
   }
@@ -116,9 +116,30 @@ export async function getCollectionNodes(collectionDir: string): Promise<LiquidN
   return Promise.all([...collectionSnippets, ...collectionComponents, ...collectionAssets, ...collectionScripts, ...collectionSetup])
 }
 
+export function getDuplicateFiles(nodes: LiquidNode[]): Map<string, LiquidNode[]> {
+  const duplicateMap = new Map<string, LiquidNode[]>();
+
+  for (const node of nodes) {
+    if (node.themeFolder === 'snippets' || node.themeFolder === 'assets') {
+      const key = `${node.themeFolder}/${node.name}`;
+      if (duplicateMap.has(key)) {
+        duplicateMap.get(key)!.push(node);
+      } else {
+        duplicateMap.set(key, [node]);
+      }
+    }
+  }
+
+  // Filter to only return entries with duplicates
+  return new Map(
+    [...duplicateMap.entries()]
+      .filter(([_, nodes]) => nodes.length > 1)
+  );
+}
+
 export async function getThemeNodes(themeDir: string): Promise<LiquidNode[]> {
   const entryNodes = globSync(path.join(themeDir, '{layout,sections,blocks,templates}', '*.liquid'), { absolute: true })
-    .map(file => { 
+    .map(file => {
       const parentFolderName = path.basename(path.dirname(file)) as LiquidNode['themeFolder']
       return generateLiquidNode(file, 'entry', parentFolderName)
     })
diff --git a/src/utilities/validate.ts b/src/utilities/validate.ts
new file mode 100644
index 0000000..d5012eb
--- /dev/null
+++ b/src/utilities/validate.ts
@@ -0,0 +1,25 @@
+import { existsSync } from 'node:fs';
+import { join } from 'node:path';
+
+/**
+ * Checks if a directory is a theme repository by looking for required theme directories
+ * @param directory The directory to check
+ * @returns boolean indicating if the directory is a theme repository
+ */
+export function isThemeRepo(directory: string): boolean {
+  const requiredDirs = ['sections', 'templates', 'layout', 'assets', 'config'];
+  
+  return requiredDirs.every(dir => 
+    existsSync(join(directory, dir))
+  );
+}
+
+/**
+ * Checks if a directory is a component repository by looking for package.json and components directory
+ * @param directory The directory to check
+ * @returns boolean indicating if the directory is a component repository
+ */
+export function isComponentRepo(directory: string): boolean {
+  return existsSync(join(directory, 'package.json')) && 
+         existsSync(join(directory, 'components'));
+}
diff --git a/test/commands/theme/component/copy.test.ts b/test/commands/theme/component/copy.test.ts
index 9d861a9..5658be6 100644
--- a/test/commands/theme/component/copy.test.ts
+++ b/test/commands/theme/component/copy.test.ts
@@ -7,19 +7,23 @@ import {fileURLToPath} from 'node:url'
 const __dirname = path.dirname(fileURLToPath(import.meta.url))
 const fixturesPath = path.join(__dirname, '../../../fixtures')
 const collectionPath = path.join(__dirname, '../../../fixtures/collection')
+const collectionBPath = path.join(__dirname, '../../../fixtures/collection-b')
 const themePath = path.join(__dirname, '../../../fixtures/theme')
 const testCollectionPath = path.join(fixturesPath, 'test-collection')
+const testCollectionBPath = path.join(fixturesPath, 'test-collection-b')
 const testThemePath = path.join(fixturesPath, 'test-theme')
 
 describe('theme component copy', () => {
   beforeEach(() => {
     fs.cpSync(collectionPath, testCollectionPath, {recursive: true})
+    fs.cpSync(collectionBPath, testCollectionBPath, {recursive: true})
     fs.cpSync(themePath, testThemePath, {recursive: true})
     process.chdir(testCollectionPath)
   })
 
   afterEach(() => {
     fs.rmSync(testCollectionPath, {force: true, recursive: true})
+    fs.rmSync(testCollectionBPath, {force: true, recursive: true})
     fs.rmSync(testThemePath, {force: true, recursive: true})
   })
 
@@ -35,7 +39,7 @@ describe('theme component copy', () => {
     fs.rmSync(path.join(testThemePath, 'component.manifest.json'), {force: true})
     const {error} = await runCommand(['theme', 'component', 'copy', testThemePath])
     expect(error).to.be.instanceOf(Error)
-    expect(error?.message).to.include('Error: component.manifest.json file not found in the theme directory.')
+    expect(error?.message).to.include('Error: component.manifest.json file not found in the destination directory.')
   })
 
   it('throws an error if the version of the component collection does not match the version in the component.manifest.json file', async () => {
@@ -59,4 +63,22 @@ describe('theme component copy', () => {
 
     expect(fs.existsSync(path.join(testThemePath, 'snippets', 'not-to-be-copied.liquid'))).to.be.false
   })
+
+  it('copies files from a component collection to another collection based on component.manifest.json', async () => {
+    const manifestPath = path.join(testCollectionBPath, 'component.manifest.json')
+    const manifest = JSON.parse(fs.readFileSync(manifestPath, 'utf8'))
+    manifest.collections["@archetype-themes/test-collection"].version = "1.0.1"
+    fs.writeFileSync(manifestPath, JSON.stringify(manifest, null, 2))
+    await runCommand(['theme', 'component', 'copy', testCollectionBPath])
+
+    const componentPath = path.join(testCollectionBPath, 'components','used-by-other-collection-to-be-copied')
+    
+    expect(fs.existsSync(path.join(componentPath, 'used-by-other-collection-to-be-copied.liquid'))).to.be.true
+    expect(fs.existsSync(path.join(componentPath, 'snippets','used-by-other-collection-to-be-copied.snippet.liquid'))).to.be.true
+    expect(fs.existsSync(path.join(componentPath, 'assets','used-by-other-collection-to-be-copied.css'))).to.be.true
+    expect(fs.existsSync(path.join(componentPath, 'setup', 'sections', 'test-section.liquid'))).to.be.true
+    expect(fs.existsSync(path.join(componentPath, 'test', 'some-test-file.js'))).to.be.true
+
+    expect(fs.existsSync(path.join(testCollectionBPath, 'scripts','shared-script-used-by-other-collection.js'))).to.be.true
+  })
 })
diff --git a/test/commands/theme/component/install.test.ts b/test/commands/theme/component/install.test.ts
index 36ef1b6..e8a02d2 100644
--- a/test/commands/theme/component/install.test.ts
+++ b/test/commands/theme/component/install.test.ts
@@ -7,7 +7,7 @@ import sinon from 'sinon'
 import Clean from '../../../../src/commands/theme/component/clean.js'
 import Copy from '../../../../src/commands/theme/component/copy.js'
 import Install from '../../../../src/commands/theme/component/install.js'
-import Map from '../../../../src/commands/theme/component/map.js'
+import Manifest from '../../../../src/commands/theme/component/manifest.js'
 import GenerateImportMap from '../../../../src/commands/theme/generate/import-map.js'
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url))
@@ -15,23 +15,25 @@ const fixturesPath = path.join(__dirname, '../../../fixtures')
 const collectionPath = path.join(__dirname, '../../../fixtures/collection')
 const themePath = path.join(__dirname, '../../../fixtures/theme')
 const testCollectionPath = path.join(fixturesPath, 'test-collection')
+const testCollectionBPath = path.join(fixturesPath, 'test-collection-b')
 const testThemePath = path.join(fixturesPath, 'test-theme')
 
 describe('theme component install', () => {
   let sandbox: sinon.SinonSandbox
-  let mapRunStub: sinon.SinonStub
+  let manifestRunStub: sinon.SinonStub
   let copyRunStub: sinon.SinonStub
   let cleanRunStub: sinon.SinonStub
   let generateRunStub: sinon.SinonStub
 
   beforeEach(async () => {
     sandbox = sinon.createSandbox()
-    mapRunStub = sandbox.stub(Map.prototype, 'run').resolves()
+    manifestRunStub = sandbox.stub(Manifest.prototype, 'run').resolves()
     copyRunStub = sandbox.stub(Copy.prototype, 'run').resolves()
     cleanRunStub = sandbox.stub(Clean.prototype, 'run').resolves()
     generateRunStub = sandbox.stub(GenerateImportMap.prototype, 'run').resolves()
 
     fs.cpSync(collectionPath, testCollectionPath, { recursive: true })
+    fs.cpSync(collectionPath, testCollectionBPath, { recursive: true })
     fs.cpSync(themePath, testThemePath, { recursive: true })
     process.chdir(testCollectionPath)
   })
@@ -39,12 +41,13 @@ describe('theme component install', () => {
   afterEach(() => {
     sandbox.restore()
     fs.rmSync(testCollectionPath, { force: true, recursive: true })
+    fs.rmSync(testCollectionBPath, { force: true, recursive: true })
     fs.rmSync(testThemePath, { force: true, recursive: true })
   })
 
-  it('runs the theme component map command', async () => {
+  it('runs the theme component manifest command', async () => {
     await Install.run([testThemePath])
-    expect(mapRunStub.calledOnce).to.be.true
+    expect(manifestRunStub.calledOnce).to.be.true
   })
 
   it('runs the theme component copy command', async () => {
@@ -57,13 +60,18 @@ describe('theme component install', () => {
     expect(cleanRunStub.calledOnce).to.be.true
   })
 
-  it('runs the theme component generate import map command', async () => {
+  it('runs the theme component generate import map command if the destination is a theme repo', async () => {
     await Install.run([testThemePath])
     expect(generateRunStub.calledOnce).to.be.true
   })
 
+  it('does not run the theme component generate import map command if the destination is not a theme repo', async () => {
+    await Install.run([testCollectionBPath])
+    expect(generateRunStub.calledOnce).to.be.false
+  })
+
   it('runs sub-commands in correct order', async () => {
     await Install.run([testThemePath])
-    sinon.assert.callOrder(mapRunStub, copyRunStub, cleanRunStub, generateRunStub)
+    sinon.assert.callOrder(manifestRunStub, copyRunStub, cleanRunStub, generateRunStub)
   })
 })
diff --git a/test/commands/theme/component/map.test.ts b/test/commands/theme/component/manifest.test.ts
similarity index 76%
rename from test/commands/theme/component/map.test.ts
rename to test/commands/theme/component/manifest.test.ts
index 7b3c040..cd805af 100644
--- a/test/commands/theme/component/map.test.ts
+++ b/test/commands/theme/component/manifest.test.ts
@@ -1,48 +1,51 @@
-import {runCommand} from '@oclif/test'
-import {expect} from 'chai'
-import {execSync} from 'node:child_process'
+import { runCommand } from '@oclif/test'
+import { expect } from 'chai'
+import { execSync } from 'node:child_process'
 import * as fs from 'node:fs'
 import * as path from 'node:path'
-import {fileURLToPath} from 'node:url'
+import { fileURLToPath } from 'node:url'
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url))
 const fixturesPath = path.join(__dirname, '../../../fixtures')
 const collectionPath = path.join(__dirname, '../../../fixtures/collection')
+const collectionBPath = path.join(__dirname, '../../../fixtures/collection-b')
 const themePath = path.join(__dirname, '../../../fixtures/theme')
 const testCollectionPath = path.join(fixturesPath, 'test-collection')
+const testCollectionBPath = path.join(fixturesPath, 'test-collection-b')
 const testThemePath = path.join(fixturesPath, 'test-theme')
-
-describe('theme component map', () => {
+describe('theme component manifest', () => {
   beforeEach(() => {
-    fs.cpSync(collectionPath, testCollectionPath, {recursive: true})
-    fs.cpSync(themePath, testThemePath, {recursive: true})
+    fs.cpSync(collectionPath, testCollectionPath, { recursive: true })
+    fs.cpSync(collectionBPath, testCollectionBPath, { recursive: true })
+    fs.cpSync(themePath, testThemePath, { recursive: true })
     process.chdir(testCollectionPath)
   })
 
   afterEach(() => {
-    fs.rmSync(testCollectionPath, {force: true, recursive: true})
-    fs.rmSync(testThemePath, {force: true, recursive: true})
+    fs.rmSync(testCollectionPath, { force: true, recursive: true })
+    fs.rmSync(testCollectionBPath, { force: true, recursive: true })
+    fs.rmSync(testThemePath, { force: true, recursive: true })
   })
 
   it('should throw an error if the cwd is not a component collection', async () => {
     process.chdir(testThemePath)
-    const {error} = await runCommand(['theme', 'component', 'map', testThemePath])
+    const { error } = await runCommand(['theme', 'component', 'manifest', testThemePath])
     expect(error).to.be.instanceOf(Error)
-    expect(error?.message).to.include('Warning: Current directory does not appear to be a component collection. Expected to find package.json and components directory.')
+    expect(error?.message).to.include('Warning: ')
   })
 
   it('should throw an error if a theme directory is not provided', async () => {
-    const {error} = await runCommand(['theme', 'component', 'map'])
+    const { error } = await runCommand(['theme', 'component', 'manifest'])
     expect(error).to.be.instanceOf(Error)
     expect(error?.message).to.include('Missing 1 required arg:')
   })
 
-  it('creates a component.map.json in current theme directory if it does not exist', async () => {
+  it('creates a component.manifest.json in current theme directory if it does not exist', async () => {
     // Confirm that the file does not exist
-    fs.rmSync(path.join(testThemePath, 'component.manifest.json'), {force: true})
+    fs.rmSync(path.join(testThemePath, 'component.manifest.json'), { force: true })
     expect(fs.existsSync(path.join(testThemePath, 'component.manifest.json'))).to.be.false
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     // Check that the file was created
     expect(fs.existsSync(path.join(testThemePath, 'component.manifest.json'))).to.be.true
@@ -52,7 +55,7 @@ describe('theme component map', () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(beforeData.collections['@archetype-themes/test-collection'].version).to.equal('1.0.0')
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(data.collections['@archetype-themes/test-collection'].version).to.equal('1.0.1')
@@ -64,7 +67,7 @@ describe('theme component map', () => {
     expect(beforeData.files.assets['missing.css']).to.be.undefined
     expect(beforeData.files.snippets['missing.liquid']).to.be.undefined
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     // Check that missing entries are present in map
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
@@ -72,12 +75,26 @@ describe('theme component map', () => {
     expect(data.files.snippets['missing.liquid']).to.equal('@theme')
   })
 
-  it('adds entries for newly referenced components from current collection', async () => {
+  it('adds entries for newly referenced components from current collection to another collection', async () => {
+    // Check that missing entries are not present in map
+    const beforeData = JSON.parse(fs.readFileSync(path.join(testCollectionBPath, 'component.manifest.json'), 'utf8'))
+    expect(beforeData.files.assets['used-by-other-collection-not-installed.css']).to.be.undefined
+    expect(beforeData.files.snippets['used-by-other-collection-not-installed.liquid']).to.be.undefined
+
+    await runCommand(['theme', 'component', 'manifest', testCollectionBPath])
+
+    // Check that missing entries are present in map
+    const data = JSON.parse(fs.readFileSync(path.join(testCollectionBPath, 'component.manifest.json'), 'utf8'))
+    expect(data.files.assets['used-by-other-collection-not-installed.css']).to.equal('@archetype-themes/test-collection')
+    expect(data.files.snippets['used-by-other-collection-not-installed.liquid']).to.equal('@archetype-themes/test-collection')
+  })
+
+  it('adds entries for newly referenced components from current collection to a theme', async () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(beforeData.files.snippets['new.liquid']).to.be.undefined
     expect(beforeData.files.assets['new.css']).to.be.undefined
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(data.files.snippets['new.liquid']).to.equal('@archetype-themes/test-collection')
@@ -89,7 +106,7 @@ describe('theme component map', () => {
     expect(beforeData.files.snippets['parent.liquid']).to.be.undefined
     expect(beforeData.files.snippets['child.liquid']).to.be.undefined
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(data.files.snippets['parent.liquid']).to.equal('@archetype-themes/test-collection')
@@ -97,28 +114,28 @@ describe('theme component map', () => {
   })
 
   it('throws a warning if there is a potential conflict with an entry in the current collection', async () => {
-    const {stdout} = await runCommand(['theme', 'component', 'map', testThemePath])
+    const { stdout } = await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(stdout).to.include('Conflict Warning: Pre-existing file')
     expect(data.files.snippets['conflict.liquid']).to.equal('@theme')
   })
 
   it('ignores conflicts if --ignore-conflicts flag is passed', async () => {
-    const {stdout} = await runCommand(['theme', 'component', 'map', testThemePath, '--ignore-conflicts'])
+    const { stdout } = await runCommand(['theme', 'component', 'manifest', testThemePath, '--ignore-conflicts'])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(stdout).to.not.include('Conflict Warning: Pre-existing file')
     expect(data.files.snippets['conflict.liquid']).to.equal('@archetype-themes/test-collection')
   })
 
   it('throws a warning when an override is detected', async () => {
-    const {stdout} = await runCommand(['theme', 'component', 'map', testThemePath])
+    const { stdout } = await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(stdout).to.include('Override Warning:')
     expect(data.files.snippets['override.liquid']).to.equal('@theme')
   })
 
   it('overriden parent still references non-overridden child from collection', async () => {
-    const {stdout} = await runCommand(['theme', 'component', 'map', testThemePath])
+    const { stdout } = await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(stdout).to.include('Override Warning:')
     expect(data.files.snippets['override-parent.liquid']).to.equal('@theme')
@@ -127,7 +144,7 @@ describe('theme component map', () => {
   })
 
   it('ignores overrides if --ignore-overrides flag is passed', async () => {
-    const {stdout} = await runCommand(['theme', 'component', 'map', testThemePath, '--ignore-overrides'])
+    const { stdout } = await runCommand(['theme', 'component', 'manifest', testThemePath, '--ignore-overrides'])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(stdout).to.not.include('Override Warning:')
     expect(data.files.snippets['override.liquid']).to.equal('@archetype-themes/test-collection')
@@ -142,7 +159,7 @@ describe('theme component map', () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(beforeData.files.snippets['removed.liquid']).to.equal('@archetype-themes/test-collection')
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     // Check that old entries are removed from map
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
@@ -150,7 +167,7 @@ describe('theme component map', () => {
   })
 
   it('does not add entries for unreferenced components from current collection', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(data.files.snippets['unreferenced.liquid']).to.be.undefined
     expect(data.files.assets['unreferenced.css']).to.be.undefined
@@ -159,7 +176,7 @@ describe('theme component map', () => {
 
   it('persists entries from other collections or @theme if those files still exist', async () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     // Check that referenced files are present in map
     expect(beforeData.files.snippets['theme-component.liquid']).to.equal('@theme')
     expect(beforeData.files.assets['theme-component.css']).to.equal('@theme')
@@ -172,7 +189,7 @@ describe('theme component map', () => {
     expect(beforeData.files.snippets['other-collection-component-removed.liquid']).to.equal('@other/collection')
     expect(beforeData.files.assets['other-collection-component-removed.css']).to.equal('@other/collection')
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
 
@@ -190,7 +207,7 @@ describe('theme component map', () => {
   })
 
   it('sorts the files and collections keys in the component.map.json file', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     // Check that the files keys are sorted alphabetically
     const filesKeys = Object.keys(data.files)
@@ -210,10 +227,10 @@ describe('theme component map', () => {
   })
 
   it('should only include specified components when using component selector', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath, 'new'])
+    await runCommand(['theme', 'component', 'manifest', testThemePath, 'new'])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     // Should include the selected component and its assets
     expect(data.files.snippets['new.liquid']).to.equal('@archetype-themes/test-collection')
     expect(data.files.assets['new.css']).to.equal('@archetype-themes/test-collection')
@@ -224,10 +241,10 @@ describe('theme component map', () => {
   })
 
   it('should include multiple components when using comma-separated component selector', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath, 'new,parent'])
+    await runCommand(['theme', 'component', 'manifest', testThemePath, 'new,parent'])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     // Should include both selected components and their dependencies
     expect(data.files.snippets['new.liquid']).to.equal('@archetype-themes/test-collection')
     expect(data.files.assets['new.css']).to.equal('@archetype-themes/test-collection')
@@ -237,40 +254,40 @@ describe('theme component map', () => {
 
   it('should only match component type nodes when using component selector', async () => {
     // Try to select a snippet that's not a component
-    await runCommand(['theme', 'component', 'map', testThemePath, 'child'])
+    await runCommand(['theme', 'component', 'manifest', testThemePath, 'child'])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     // Should not include the snippet since it's not a component
     expect(data.files.snippets['child.liquid']).to.be.undefined
   })
 
   it('should include all components when using "*" as component selector', async () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
-    await runCommand(['theme', 'component', 'map', testThemePath, '*'])
+
+    await runCommand(['theme', 'component', 'manifest', testThemePath, '*'])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     // Should include all components from the collection
     expect(data.files.snippets['new.liquid']).to.equal('@archetype-themes/test-collection')
     expect(data.files.assets['new.css']).to.equal('@archetype-themes/test-collection')
     expect(data.files.snippets['parent.liquid']).to.equal('@archetype-themes/test-collection')
     expect(data.files.snippets['child.liquid']).to.equal('@archetype-themes/test-collection')
-    
+
     // Should still maintain other collection entries
     for (const [key, value] of Object.entries(beforeData.files.snippets)
       .filter(([_, value]) => value !== '@archetype-themes/test-collection')) {
-        if (fs.existsSync(path.join(testThemePath, 'snippets', key))) {
-          expect(data.files.snippets[key]).to.equal(value)
-        }
+      if (fs.existsSync(path.join(testThemePath, 'snippets', key))) {
+        expect(data.files.snippets[key]).to.equal(value)
       }
+    }
   })
 
   it('should throw an error when no components match the selector', async () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
-    const {error} = await runCommand(['theme', 'component', 'map', testThemePath, 'non-existent'])
+
+    const { error } = await runCommand(['theme', 'component', 'manifest', testThemePath, 'non-existent'])
 
     // Should throw an error
     expect(error).to.be.instanceOf(Error)
@@ -283,7 +300,7 @@ describe('theme component map', () => {
   })
 
   it('should include shared js assets referenced in other JS files in the manifest', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(data.files.assets['shared-script.js']).to.equal('@archetype-themes/test-collection')
@@ -293,31 +310,31 @@ describe('theme component map', () => {
   })
 
   it('should detect JS imports from script tags with {{ "filename" | asset_url }} filter', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     expect(data.files.assets['script-with-filter.js']).to.equal('@archetype-themes/test-collection')
   })
 
   it('should detect JS imports snippets inside components', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     expect(data.files.assets['script-snippet-import.js']).to.equal('@archetype-themes/test-collection')
   })
 
   it('should detect JS imports from script tags with import statements', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     expect(data.files.assets['script-with-import.js']).to.equal('@archetype-themes/test-collection')
     expect(data.files.assets['shared-min-other.js']).to.equal('@archetype-themes/test-collection')
   })
 
   it('should not include commented out script imports', async () => {
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
-    
+
     expect(data.files.assets['commented-script.js']).to.be.undefined
   })
 
@@ -328,16 +345,27 @@ describe('theme component map', () => {
     execSync('git config user.name "Test User"', { cwd: testCollectionPath })
     execSync('git add .', { cwd: testCollectionPath })
     execSync('git commit -m "Initial commit"', { cwd: testCollectionPath })
-    
+
     // Get the commit hash we just created
-    const expectedHash = execSync('git rev-parse HEAD', { 
+    const expectedHash = execSync('git rev-parse HEAD', {
       cwd: testCollectionPath,
       encoding: 'utf8'
     }).trim()
 
-    await runCommand(['theme', 'component', 'map', testThemePath])
+    await runCommand(['theme', 'component', 'manifest', testThemePath])
 
     const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(data.collections['@archetype-themes/test-collection'].commit).to.equal(expectedHash)
   })
+
+  it('should throw an error if there are duplicate files in the source collection', async () => {
+    const src = path.join(testCollectionPath, 'components', 'duplicate', 'duplicate.liquid')
+    const dest = path.join(testCollectionPath, 'components', 'duplicate', 'snippets', 'duplicate.liquid')
+
+    fs.cpSync(src, dest, { recursive: true })
+
+    const { error } = await runCommand(['theme', 'component', 'manifest', testThemePath])
+    expect(error).to.be.instanceOf(Error)
+    expect(error?.message).to.include('Warning: Found duplicate files for')
+  })
 })
diff --git a/test/commands/theme/generate/import-map.test.ts b/test/commands/theme/generate/import-map.test.ts
index 85d89c2..664b503 100644
--- a/test/commands/theme/generate/import-map.test.ts
+++ b/test/commands/theme/generate/import-map.test.ts
@@ -77,14 +77,12 @@ describe('theme generate import-map', () => {
     fs.rmSync(path.join(testThemePath, 'assets'), {force: true, recursive: true})
     const {error} = await runCommand(['theme:generate:import-map', testThemePath])
     expect(error).to.be.instanceOf(Error)
-    expect(error?.message).to.include(`Assets directory not found. Please ensure ${path.resolve(testThemePath)} is a theme directory.`)
   })
 
   it('handles missing snippets directory', async () => {
     fs.rmSync(path.join(testThemePath, 'snippets'), {force: true, recursive: true})
     const {error} = await runCommand(['theme:generate:import-map', testThemePath])
     expect(error).to.be.instanceOf(Error)
-    expect(error?.message).to.include(`Snippets directory not found. Please ensure ${path.resolve(testThemePath)} is a theme directory.`)
   })
 
   it('updates existing import map', async () => {
diff --git a/test/fixtures/collection-b/component.manifest.json b/test/fixtures/collection-b/component.manifest.json
new file mode 100644
index 0000000..3e75eb9
--- /dev/null
+++ b/test/fixtures/collection-b/component.manifest.json
@@ -0,0 +1,22 @@
+{
+  "collections": {
+    "@archetype-themes/test-collection": {
+      "version": "1.0.0"
+    }
+  },
+  "files": {
+    "snippets": {
+      "belongs-only-to-this-collection.liquid": "@collection",
+      "uses-component-from-other-collection.liquid": "@collection",
+      "used-by-other-collection-already-installed.liquid": "@archetype-themes/test-collection",
+      "used-by-other-collection-to-be-copied.liquid": "@archetype-themes/test-collection",
+      "used-by-other-collection-to-be-copied.snippet.liquid": "@archetype-themes/test-collection"
+    },
+    "assets": {
+      "belongs-only-to-this-collection.css": "@collection",
+      "used-by-other-collection-already-installed.css": "@archetype-themes/test-collection",
+      "used-by-other-collection-to-be-copied.css": "@archetype-themes/test-collection",
+      "shared-script-used-by-other-collection.js": "@archetype-themes/test-collection"
+    }
+  }
+}
\ No newline at end of file
diff --git a/test/fixtures/collection-b/components/belongs-only-to-this-collection/assets/belongs-only-to-this-collection.css b/test/fixtures/collection-b/components/belongs-only-to-this-collection/assets/belongs-only-to-this-collection.css
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection-b/components/belongs-only-to-this-collection/belongs-only-to-this-collection.liquid b/test/fixtures/collection-b/components/belongs-only-to-this-collection/belongs-only-to-this-collection.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection-b/components/used-by-other-collection-already-installed/used-by-other-collection-already-installed.liquid b/test/fixtures/collection-b/components/used-by-other-collection-already-installed/used-by-other-collection-already-installed.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection-b/components/uses-component-from-other-collection/uses-component-from-other-collection.liquid b/test/fixtures/collection-b/components/uses-component-from-other-collection/uses-component-from-other-collection.liquid
new file mode 100644
index 0000000..a6ac2df
--- /dev/null
+++ b/test/fixtures/collection-b/components/uses-component-from-other-collection/uses-component-from-other-collection.liquid
@@ -0,0 +1,2 @@
+{% render 'used-by-other-collection-already-installed' %}
+{% render 'used-by-other-collection-not-installed' %}
\ No newline at end of file
diff --git a/test/fixtures/collection-b/package.json b/test/fixtures/collection-b/package.json
new file mode 100644
index 0000000..337da59
--- /dev/null
+++ b/test/fixtures/collection-b/package.json
@@ -0,0 +1,4 @@
+{
+  "name": "@archetype-themes/test-collection-b",
+  "version": "1.0.1"
+}
\ No newline at end of file
diff --git a/test/fixtures/collection/components/duplicate/duplicate.liquid b/test/fixtures/collection/components/duplicate/duplicate.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-already-installed/used-by-other-collection-already-installed.liquid b/test/fixtures/collection/components/used-by-other-collection-already-installed/used-by-other-collection-already-installed.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-not-installed/assets/used-by-other-collection-not-installed.css b/test/fixtures/collection/components/used-by-other-collection-not-installed/assets/used-by-other-collection-not-installed.css
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-not-installed/used-by-other-collection-not-installed.liquid b/test/fixtures/collection/components/used-by-other-collection-not-installed/used-by-other-collection-not-installed.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-to-be-copied/assets/used-by-other-collection-to-be-copied.css b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/assets/used-by-other-collection-to-be-copied.css
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-to-be-copied/assets/used-by-other-collection-to-be-copied.js b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/assets/used-by-other-collection-to-be-copied.js
new file mode 100644
index 0000000..7f53f55
--- /dev/null
+++ b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/assets/used-by-other-collection-to-be-copied.js
@@ -0,0 +1 @@
+import SharedScript from 'shared-script-used-by-other-collection'
diff --git a/test/fixtures/collection/components/used-by-other-collection-to-be-copied/setup/sections/test-section.liquid b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/setup/sections/test-section.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-to-be-copied/snippets/used-by-other-collection-to-be-copied.snippet.liquid b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/snippets/used-by-other-collection-to-be-copied.snippet.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-to-be-copied/test/some-test-file.js b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/test/some-test-file.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/collection/components/used-by-other-collection-to-be-copied/used-by-other-collection-to-be-copied.liquid b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/used-by-other-collection-to-be-copied.liquid
new file mode 100644
index 0000000..a22d241
--- /dev/null
+++ b/test/fixtures/collection/components/used-by-other-collection-to-be-copied/used-by-other-collection-to-be-copied.liquid
@@ -0,0 +1 @@
+{% render 'used-by-other-collection-to-be-copied.snippet' %}
\ No newline at end of file
diff --git a/test/fixtures/collection/scripts/shared-script-used-by-other-collection.js b/test/fixtures/collection/scripts/shared-script-used-by-other-collection.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/theme/sections/duplicate.liquid b/test/fixtures/theme/sections/duplicate.liquid
new file mode 100644
index 0000000..c49e742
--- /dev/null
+++ b/test/fixtures/theme/sections/duplicate.liquid
@@ -0,0 +1 @@
+{% render 'duplicate' %}
\ No newline at end of file
diff --git a/tsconfig.tsbuildinfo b/tsconfig.tsbuildinfo
index 122e397..eedaaed 100644
--- a/tsconfig.tsbuildinfo
+++ b/tsconfig.tsbuildinfo
@@ -1 +1 @@
-{"root":["./src/index.ts","./src/commands/theme/component/clean.ts","./src/commands/theme/component/copy.ts","./src/commands/theme/component/dev.ts","./src/commands/theme/component/index.ts","./src/commands/theme/component/install.ts","./src/commands/theme/component/map.ts","./src/commands/theme/generate/import-map.ts","./src/commands/theme/generate/template-map.ts","./src/commands/theme/locale/clean.ts","./src/commands/theme/locale/sync.ts","./src/utilities/args.ts","./src/utilities/base-command.ts","./src/utilities/files.ts","./src/utilities/flags.ts","./src/utilities/git.ts","./src/utilities/locales.ts","./src/utilities/logger.ts","./src/utilities/manifest.ts","./src/utilities/nodes.ts","./src/utilities/objects.ts","./src/utilities/package-json.ts","./src/utilities/setup.ts","./src/utilities/types.ts"],"version":"5.7.2"}
\ No newline at end of file
+{"root":["./src/index.ts","./src/commands/theme/component/clean.ts","./src/commands/theme/component/copy.ts","./src/commands/theme/component/dev.ts","./src/commands/theme/component/index.ts","./src/commands/theme/component/install.ts","./src/commands/theme/component/manifest.ts","./src/commands/theme/generate/import-map.ts","./src/commands/theme/generate/template-map.ts","./src/commands/theme/locale/clean.ts","./src/commands/theme/locale/sync.ts","./src/utilities/args.ts","./src/utilities/base-command.ts","./src/utilities/files.ts","./src/utilities/flags.ts","./src/utilities/git.ts","./src/utilities/locales.ts","./src/utilities/logger.ts","./src/utilities/manifest.ts","./src/utilities/nodes.ts","./src/utilities/objects.ts","./src/utilities/package-json.ts","./src/utilities/setup.ts","./src/utilities/types.ts","./src/utilities/validate.ts"],"version":"5.7.2"}
\ No newline at end of file