You can achieve FileType association in Cordova.
It includes 2 steps.
1) register files in Android Manifest / iOS plist as
Manifest
<intent-filter
android:icon='@drawable/ic_launcher'
android:label='AndroidMHT File'
android:priority='1'>
<action android:name="android.intent.action.VIEW" />
<action android:name="android.intent.action.EDIT" />
<action android:name="android.intent.action.PICK" />
<category android:name="android.intent.category.DEFAULT" />
<category android:name="android.intent.category.BROWSABLE" />
<data android:mimeType="*/*" />
<data android:pathPattern="*.mht" />
</intent-filter>
<intent-filter>
<action android:name="android.intent.action.VIEW" />
<category android:name="android.intent.category.DEFAULT" />
<category android:name="android.intent.category.BROWSABLE" />
<data android:scheme="http" android:host="*" android:pathPattern=".*\.mht" />
<data android:scheme="https" android:host="*" android:pathPattern=".*\.mht" />
</intent-filter>
<intent-filter>
<action android:name="android.intent.action.VIEW" />
<category android:name="android.intent.category.DEFAULT" />
<category android:name="android.intent.category.BROWSABLE" />
<data android:mimeType="message/rfc822" android:scheme="http" />
<data android:mimeType="multipart/related" android:scheme="http" />
<data android:mimeType="message/rfc822" android:scheme="https" />
<data android:mimeType="multipart/related" android:scheme="https" />
</intent-filter>
plist
<key>CFBundleDocumentTypes</key>
<array>
<dict>
<key>CFBundleTypeIconFiles</key>
<array>
<string>Document-molecules-320.png</string>
<string>Document-molecules-64.png</string>
</array>
<key>CFBundleTypeName</key>
<string>Molecules Structure File</string>
<key>CFBundleTypeRole</key>
<string>Viewer</string>
<key>LSHandlerRank</key>
<string>Owner</string>
<key>LSItemContentTypes</key>
<array>
<string>com.sunsetlakesoftware.molecules.pdb</string>
<string>org.gnu.gnu-zip-archive</string>
</array>
</dict>
</array>
2) Use the File Opener Plugin for Cordova
You may need to pass necessary flags to open those files.
Reference: Android, iOS and a phonegap community forum thread
Hope it helps.
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