Re-seed bundled core packages when content changes at the same version#113
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seedBundledPackage only re-extracted a bundled core package (BEAST.base, BEAST.app) into the user package dir when the bundled version was strictly newer than the copy already there. The package version string stays constant across a release cycle (e.g. 2.8.0), so after `mvn package` plus a fresh application build the stale lib/ was kept and the running app loaded pre-fix classes -- which is why the BEAUti Template menu fix (#110) worked in a developer environment but not in the installed app. When the user copy reports the same version as the bundled one, fall back to comparing a SHA-256 of the bundled zip against a marker recorded at seed time, and re-extract on mismatch. Versions that differ are still decided by number alone: a strictly newer user copy is never downgraded, a strictly older one is always replaced. The checksum is computed only when the versions match or when re-seeding. Fixes #112
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Problem
The BEAUti Template menu fix (#110, merged in #111) worked in a developer environment but the menu was still empty in the installed app (#112). The fix code was correct; it never reached the running app.
The release ships
BEAST.base/BEAST.appas package zips thatBeastLauncher.seedBundledPackage()extracts into the user package dir and loads as plugin module layers. That method only re-extracted when the bundled version was strictly newer than the copy already seeded. The package version string (version.xml) is constant across a release cycle (2.8.0), so aftermvn package+ a fresh build the stalelib/was kept and the app kept loading pre-fix classes. (Confirmed: the crash trace in #112 matches pre-fix line numbers.)Fix
When the user copy reports the same version as the bundled one, compare a SHA-256 of the bundled zip against a marker (
.bundled.checksum) written at seed time, and re-extract on mismatch. This catches development rebuilds and re-released betas, not just SNAPSHOTs.Differing versions are still decided by number alone — a strictly newer user copy (e.g. a package-manager upgrade) is never downgraded, a strictly older one is always replaced. The checksum is computed only when versions match or when re-seeding.
Tests
SeedBundledPackageReseedTest(new): same-version-new-content re-seeds, identical zip is left untouched, strictly-newer user copy is preserved. ExistingSeedBundledPackageTeststill passes.Fixes #112