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Timothy thanks for your input.
I am using OTHER_CODE_SIGN_FLAGS with the plugin. It works for me in combination of using the developer profile. What problems are you having with it ? My main issue is that it makes it more cumbersome for job configuration. Note: the OTHER_CODE_SIGN_FLAGS only work if the keychain as also been added to the search list! From the codesign documentation
SIGNING IDENTITIES
To be used for code signing, a digital identity must be stored in
a keychain that is on the calling user's keychain search list.
See http://prod.lists.apple.com/archives/xcode-users/2014/Dec/msg00041.html
WRT atomicity, see http://lists.apple.com/archives/xcode-users/2014/Dec/msg00040.html to which someone answered to me offlist with 'man lockfile'for an idea on how to implement adding this in an atomic way
See also https://github.com/jenkinsci/xcode-plugin/pull/56 for a pull request that I received with similar intent, and closed because I didn't like the implementation.
To summarise,
I don't know yet how to solve it cleanly, and I don't know which use cases are the most important for the people. See also https://groups.google.com/d/msg/jenkinsci-dev/JrHvfNc3cQI/a4rAY1L8Ug0J for my request for input, so far without feedback.