Apps that has been installed from the AppStore are already signed by Apple and therefor can be run on the iOS, but if you done any changes to a IPA or install a 3rd party app you would need to sign it.

Another good guide to signing application can be found in the Objection Wiki:

https://github.com/sensepost/objection/wiki/Patching-iOS-Applications

To resign the application we would need to use applesign with a certificate

Generating certificate

Generate a new iOS certificate using xcode (see Objection link above)

Extract the code signing certificate:

security find-identity -v -p codesigning

applesign

Note: if you getting error signing see 'Errors' Page

install: npm install -g applesign

Mobexler@Mobexler  /tmp  applesign          
Usage:

  applesign [--options ...] [target.ipa | Payload/Target.app]

  -a, --all                     Resign all binaries, even it unrelated to the app
  -b, --bundleid [BUNDLEID]     Change the bundleid when repackaging
  -c, --clone-entitlements      Clone the entitlements from the provisioning to the bin
  -f, --force-family            Force UIDeviceFamily in Info.plist to be iPhone
  -h, --help                    Show verbose help message
  -H, --allow-http              Add NSAppTransportSecurity.NSAllowsArbitraryLoads in plist
  -i, --identity [1C4D1A..]     Specify hash-id of the identity to use
  -L, --identities              List local codesign identities
  -m, --mobileprovision [FILE]  Specify the mobileprovision file to use
  -o, --output [APP.IPA]        Path to the output IPA filename
  -O, --osversion 9.0           Force specific OSVersion if any in Info.plist
  -p, --without-plugins         Remove plugins (excluding XCTests) from the resigned IPA
  -w, --without-watchapp        Remove the WatchApp from the IPA before resigning
  -x, --without-xctests         Remove the XCTests from the resigned IPA

Example:

  $ applesign -w -c -m embedded.mobileprovision target.ipa

Signing example with applesign

iron@MacOS / %  applesign SimpleApp_decrypted.ipa -B -c -d --identity R4G******* --mobileprovision embedded.mobileprovision -o signed_SimpleApp.ipa
File: /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa
Outdir: /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79
Cleaning up /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79
Unzipping /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa
Main IPA executable is not encrypted
Embedding new mobileprovision
{"application-identifier":"6B****.*","keychain-access-groups":["6B****.*","com.apple.token"],"get-task-allow":true,"com.apple.developer.team-identifier":"6B****"}
Cloning entitlements
get-task-allow set to true
Updated binary entitlements/var/folders/78/n8glt3614dq4b9jl0zszs_yh0000gn/T/applesign/24dde536-1343-4024-8095-de6e21f53bcf/SimpleApp.entitlements
Signing libraries and frameworks
Resolving signing order using layered list
[
  '/Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/PlugIns/MostWatchedWidget.appex/MostWatchedWidget',
  '/Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/PlugIns/iMessageExtension.appex/iMessageExtension'
]
Cannot resolve rpath for: @rpath/libswiftAVFoundation.dylib from /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/SimpleApp
Warning: Cannot resolve dependency library: /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/SimpleApp
Cannot resolve rpath for: @rpath/libswiftAccelerate.dylib from /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/SimpleApp
Warning: missing file: @rpath/libswiftAVFoundation.dylib
{"application-identifier":"6B****.*","keychain-access-groups":["6B****.*","com.apple.token"],"get-task-allow":true,"com.apple.developer.team-identifier":"6B****"}
Cloning entitlements
get-task-allow set to true
Updated binary entitlements/var/folders/78/n8glt3614dq4b9jl0zszs_yh0000gn/T/applesign/24dde536-1343-4024-8095-de6e21f53bcf/MostWatchedWidget.entitlements
Signed /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/PlugIns/MostWatchedWidget.appex/MostWatchedWidget
{"application-identifier":"6B****.*","keychain-access-groups":["6B****.*","com.apple.token"],"get-task-allow":true,"com.apple.developer.team-identifier":"6B****"}
Cloning entitlements
get-task-allow set to true
Updated binary entitlements/var/folders/78/n8glt3614dq4b9jl0zszs_yh0000gn/T/applesign/24dde536-1343-4024-8095-de6e21f53bcf/iMessageExtension.entitlements
Signed /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/Frameworks/Services.framework/Services
Signed /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79/Payload/SimpleApp.app/Frameworks/protobuf.framework/protobuf
Zipifying into /Users/iron/Documents/Project/SimpleApp/signed_SimpleApp.ipa ...
Cleaning up /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79
Target is now signed: /Users/iron/Documents/Project/SimpleApp/signed_SimpleApp.ipa
Cleaning up temp dir /var/folders/78/n8glt3614dq4b9jl0zszs_yh0000gn/T/applesign/24dde536-1343-4024-8095-de6e21f53bcf
Cleaning up /Users/iron/Documents/Project/SimpleApp/SimpleApp_decrypted.ipa.25115fb8-5a1f-4ed9-8ab4-6f13136d8a79

Inject Frida Gadget

Objection

Note: if you getting error signing see 'Errors' Page

Install: sudo pip3 install objection