Migrate dune-project files to tangled source format

Convert all packages from:
(source (uri https://tangled.org/handle/repo))
to:
(source (tangled handle/repo))

This uses dune 3.21's native tangled support for cleaner source
declarations. Also removes redundant homepage/bug_reports fields
that are auto-generated from tangled sources.

dune-project

···
 (name prune)
 (generate_opam_files true)
 
-(source
- (github samoht/prune))
+(source (github samoht/prune))
 
 (authors "the Prune developers")