Fix dune test: tree list/to_concrete, scitt MST proofs, misc

- irmin/lib/tree.ml: list() now returns in-memory children even when
force_node fails; to_concrete() recursively loads backend entries
instead of dropping them silently (the placeholder None was eating
all backend-stored subtree content, so git-backed checkout → add
→ commit was losing records).
- irmin/lib/irmin: add Irmin.tree_hash and Irmin.prove — both backends
expose inclusion proofs via a new prove method on the S signature.
Git uses Private.Proof.Git.produce, Mst uses Private.Proof.Mst.produce;
prove returns the CBOR-encoded proof bytes + the value at the key.
- ocaml-scitt/lib/atp/scitt_atp.ml: the MST VDS was returning path = []
as a placeholder, so every receipt failed verification. Now produces
a real Irmin.prove-generated inclusion proof, wraps it in
[repo_key; proof_bytes] CBOR, and uses the tree-root CID (not the
commit hash) as the receipt root.
- ocaml-mbr/lib/mbr.ml: to_string used Bytes.create which is not
guaranteed to be zeroed; unused partition slots carried uninitialised
bytes and the roundtrip fuzz test broke. Use Bytes.make '\x00'.
- ocaml-tls/eio/tests/tls_eio.md: MDX could not resolve the virtual
crypto library from #require "crypto-rng.unix" alone; explicitly
require crypto.c first so the default implementation is loaded.
- irmin/test/dune: git.t was not wired into the cram stanza, so the
test was using whichever irmin binary happened to be on PATH instead
of the freshly built one.