So I finally settled on using a swift package to handle the command line tool project, which I added to the main app project using the package dependencies. This package executable product could be set as a dependency, and I added a run script build phase to sign the tool and embed it in the main app's Resources folder. The SPM executable product needs to be signed with --options=runtime to be embedded in a notarized macOS app. The script is pretty simple: #!/bin/bash devID="Developer ID Application: Me Myself (ASDF1234)" toolPath="${BUILT_PRODUCTS_DIR}/MyTool" codesign --force --options=runtime --sign "${devID}" "${toolPath}" cp "${toolPath}" "${CONFIGURATION_BUILD_DIR}/${CONTENTS_FOLDER_PATH}/Resources"

I have also run into this problem with an app using a 3rd party framework. Building and running the app with Xcode 14 works fine, building and running with Xcode 15 produces team ID errors on the 3rd party framework and it doesn't load. I also tried stripping the code signatures and re-signing the framework but it still didn't load properly.

Just wanted to add that defaults write com.apple.dt.Xcode IDEPackageSupportUseBuiltinSCM YES fixed this problem for me in Xcode 26 as well, which refused to update private packages from BitBucket Cloud.