Given a pom without a <build> tag, clj -Spom will put the <sourceDirectory> tag under <project>, not under <project><build>.
Given pom.xml:
clj -Spom (no deps.edn) generates:
The <sourceDirectory> tag there should be inside a <build>.
clj 1.10.1.536
Fixed in master for next release
Released in tools.deps.alpha 0.8.695 and clj 1.10.1.536
Sorry, that should have been clj 1.10.1.547