What
Bootstrap configuration is the per-user setup information handed to the app when it starts. The code that describes its format adds a second, flat version called bootstrap-config-v1, built by buildFlatBootstrapJsonSchema.
Each setting, and some of the individual choices a setting allows, is now tagged with the first Desktop release that understands it. Examples include the mantle choice for inferenceProvider and the workforce and oauth choices for credential kind. The rules for overriding models per group moved into a separate part of the code.
Why
The version tags record which Desktop releases can read a given setting or choice, so a configuration using a newer choice can be matched against the app versions that support it.
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The finding does not say whether anything in Claude Code already sends or reads the flat v1 format.