Handle Jandex 3

[barchetta]

In Helidon 4 we plan on upgrading Jandex to 3.x. See helidon-io/helidon#6561

It has been reported that in jlink support if it can't read the Jandex index it will re-generate it. This means on a 4.x project it would overwrite the Jandex 3 index with a Jandex 2 index.

We need to either upgrade Jandex support in build-tools to 3.x, or somehow mitigate this issue.

[romain-grecourt]

actually the switch to Jandex 3.x was done in #956; this is probably incompatible with Helidon 3.x.

We should back-out the update and start a build-tools 4.x branch.

[tvallin]

Done by @romain-grecourt in #966 and #973