E505: add missing .mli files for merlint/lib/sexp, monopam-info, and
monopam/lib/{add,clean,ctx,diff,init,pull,push,remove}.
E510: add log source to ca-certs/test/tests.ml.
E410: fix doc ending period in kdf/scrypt.
E415: add pp to ocaml-agent config and runtime_config.
E331: remove redundant get_/make_/find_/create_ prefixes.
E320: remove redundant module prefixes (Diff.diff→compute,
Pull.pull→run, Push.push→run, Remove.remove→run, etc).

Add pp pretty-printers to Config and Runtime_config modules to satisfy
E415 missing pretty-printer lint rule. Fix trailing period in scrypt.mli
doc comment.

E410: Fix documentation style in 14 .mli files — add [name args] format,
correct function names (create→v, scrypt_kdf→scrypt), fix arg counts
for tuple params and pp functions, add trailing periods.

E400/E600: Add per-module log sources (ca-certs), restructure kdf and
monopam tests to use suite convention with proper .mli files, add
missing .mli files for monopam command modules.

Extract helpers in irmin/lib/git_interop.ml (E005), add module and value
docs (E400/E405), flatten test suites to single tuples (E600), add missing
test files and .mli exports (E605), fix Fpath type in e610.ml.

Replace deprecated c_names/c_flags with foreign_stubs stanza
for dune 3.21 compatibility.

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.

Fix monopam warnings about missing source stanzas and ca-certs parse error.