Generate .opam.template files with x-quality-* fields based on
detected package features:
- x-quality-build: has lib/ with .ml files
- x-quality-test: has test/ with .ml files
- x-quality-fuzz: has fuzz/ with .ml files
- x-quality-interop: has test/interop/ directory
- x-quality-cram: has test/*.t/ directories

These fields are picked up by dune's opam generation and will be
checked by merlint E910 for consistency.

Also: add fmt dep to ocaml-sse/lib/dune (Fmt.pf used without dep).

monopam quality — scans packages for quality features, caches by
git commit hash. 166 packages: build=163, test=162, fuzz=94,
interop=39, doc=42.

Standard vocabulary based on crates.io categories, erratique/opam
conventions, and monorepo domain coverage:

Org: org:blacksun
Domain: aerospace, codec, crypto, network, storage, git, merkle
Purpose: cli, test, bench, format, log, system
Protocol: ccsds, uslp, cop1, sdls, sle, atproto, tls, http, json, binary
Cross-cutting: eio, simulation, math, compression

Tags placed in dune-project (package ...) stanzas via (tags ...).
Propagated to .opam files by dune's opam generation.

- Add missing .ocamlformat to 4 packages (E500)
- stix: use Fmt.failwith instead of failwith (Fmt.str ...) (E700)
- mbr: rename _unused1/_unused2 fields — underscore prefix implies
unused but they're stored in the record (E726)

Creates c/gen.ml + c/dune + generated .3d files for every package
that defines Wire codecs. Each gen.ml calls Wire_3d.main to project
the OCaml Wire codec definition to EverParse 3D format.

Packages: FSR, PUS, GPT, MBR, PID1, LTP, TCPCL (8 codecs), UDPCL,
AX.25, CFDP (3 fixed-size codecs), SDLS (EP header + MC status),
SpaceWire, RPMsg, SquashFS (5 codecs), SpaceFibre.

Codecs with Wire.Param.input (variable-size) are excluded from 3D
generation: CFDP header/eof/metadata/keep-alive, SDLS security
header/trailer, PUS tm_header/hk_param.

Proximity-1 and space-wire excluded: proximity-1 has only variable-
size codecs, space-wire has its own C generation approach.

Fixes E900 (17→2) and E905 (remaining MBR Partition.struct_).

- Move backends into irmin/lib/{git,json,cbor,tar,atproto,oci}/
- Rename parse→dec, serialize→enc across Schema API
- Add Irmin.SHA1, Irmin.SHA256 pre-built schema instances
- Deduplicate Schema.Make boilerplate in json, cbor, tar, oci
- Implement structural diff and 4-point ddiff (was stubs)
- Implement JSON serialize via Jsont, CBOR serialize via Cbort
- Rewrite ATProto backend: Schema.Make + Heap.BACKEND + MST bridge
- Rewrite OCI backend: SHA256 JSON schema
- Rewrite all 13 bin commands for Schema/Heap API
- Fix test infrastructure: restrict old tests, rewrite mst_proof
- Fix ocaml-scitt for dec/enc rename
- Two-phase merge API: cursor * conflict list (not Ok/Error)
- Irmin.Merge module with typed combinators + v/v_result lifters
- 11 tests pass (6 schema + 5 tar), mst_proof verified

These Wire EverParse projection symbols belong in c/gen.ml (the
build-time 3D generator), not in the package's public API.

Affected: TM, TC, USLP, Space Packet, GPT, MBR, AOS, CLCW, PID1.

The codec itself remains the public API. The 3D/C generation is a
build artifact that downstream users never call directly.

Migrate all remaining binary protocol packages to use Wire codecs
for encode/decode, replacing manual Char.code / set_u8 / get_u16_be
/ put_u32_be byte-picking with Wire.Codec, Wire.map, Wire.Param,
and Wire.optional.

Packages migrated:

- cfdp: Wire codecs for 6 directive types (EOF, Finished, ACK,
Metadata, Prompt, Keep-Alive) with Param.input for large_file
flag and fss_size = 4 + 4*large_file. NAK uses be_bytes_to_int64
for the gap list (Wire.repeat blocked on byte budget from outer
PDU). 41 lines of byte helpers removed.

- sdls: Wire codecs for MC status reply, log/erase/self-test
replies, TLV event encoding. Security header/trailer use
Param.input for iv_len, sn_len, mac_len with byte_array ~size.
85 lines of byte helpers removed.

- ax25: FCS encode/decode via Wire.uint16 (LE). Extension tag
and cancel reason via Wire.map. 14 lines removed.

- proximity1: Staged Wire.Codec.get for frame-type bitfield
extraction, replacing manual bitmask. 4 lines removed.

- ltp: Wire.map for extension_tag and cancel_reason enum fields.
SDNV codec kept (variable-length encoding, not expressible as
Wire type). 3 lines removed.

- pus: Wire codecs for HK parameter, u16be field access. All
PUS secondary header encode/decode through Wire. 7 lines removed.

- mbr: Full 512-byte MBR Wire.Codec with embedded Wire.codec
for partition entries. 18 lines of byte helpers removed.

- pid1: Direct Bytes.of_string to Wire.Codec.decode, eliminating
intermediate buffer copy. 1 line removed.

- uslp: Wire.map helpers (be_uint) for variable-length integer
conversions; fecf_of_string/fecf_to_string cleaned up.

Total: ~170 lines of manual byte-picking eliminated across the
monorepo. Every binary protocol now uses Wire for format parsing.
The remaining Char.code usage is in: SDNV codec (LTP, inherently
variable-length), crypto operations (SDLS CMAC/hex), and value
conversions on Wire-decoded byte arrays.

All tests pass across all packages.

- 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.

- Update .ocamlformat to 0.29.0 across all 591 files
- csvt: reuse single Buffer.t for field reads (no alloc per field)
- sexpt: Obj members decoded from stream into Dict, typed Variant GADT
- Reformat all source files for 0.29.0

Migrate all consumers to the new wire API:
- wire.c library → wire.3d (Wire_c → Wire_3d)
- Wire.struct_/module_ → Wire.Everparse.struct_/module_
- Wire.Codec: record/|+/seal → Codec.v with Field.v and $
- Wire.bf_uint* → Wire.U8/U16/U16be/U32/U32be
- Wire.UInt32 → Wire.Private.UInt32
- Wire.cases → Wire.lookup, Wire.map now uses labeled args
- Wire.Codec.decode now returns result
- Add wire pin to root.opam.template

import used List.find_opt on raw map pairs, so a duplicate
"version" or "entries" key would shadow later occurrences.
Now checks for byte-equal duplicate keys before field extraction,
consistent with the receipt parser's cbor_check_unique_keys.

Ensure all 67 fuzz/dune files include gen_corpus.exe in the (alias fuzz)
rule deps for AFL corpus generation. Adds both missing runtest and fuzz
rules to ocaml-cose which had neither.

- Remove vendored crowbar/ directory
- Replace all Crowbar references with Alcobar across 176 .ml files
- Update all fuzz dune files: crowbar → alcobar in libraries
- Remove 77 gen_corpus.ml files (alcobar handles corpus internally)
- Update dune-project files: crowbar → alcobar in dependencies
- Update merlint rules (e705, e726): Crowbar → Alcobar in checks,
docs, and examples
- Update merlint generated docs (index.html)

428 files changed, ~1200 lines removed net.

Adds 108 missing dependency declarations across 52 packages.
Most common missing dep was fmt (38 packages), followed by wire,
eio, and bytesrw. Also improves lint output with tty tables and
better subtree filtering display.

Rename make_superblock → superblock, make_inode_buf → inode_buf,
make_image → image, make_key → key in squashfs and streaming-aead.

Add doc comments for fuzz suite values and squashfs extended codec
values.

Standardize fuzz and test conventions across 30+ packages:

- E715/E718: Add fuzz.ml runners referencing Fuzz_*.suite instead of
calling Fuzz_*.run() directly; update dune files accordingly
- E725: Fix fuzz_paseto suite name from "crowbar" to "paseto"
- E600: Create .mli interfaces for test modules (test_firmware,
test_remoteproc, test_pbkdf2, test_paseto) with single-group suites
- E605: Add missing test files (test_skills, test_monitor, test_openamp,
test_xrpc_server) with proper module extraction from inline test.ml
- E415: Add pp pretty-printer to xrpc_server type t
- E405: Add doc comment for pp_sync_action in skills.mli
- E205: Replace Printf with Fmt in fuzz_paseto and gen_corpus
- E331: Rename make_key to key in fuzz_paseto

- Change `run` signature to `string -> (string * test_case list) list -> unit`
matching Alcotest's grouping convention
- Fix `_name` bug: pass the name through to Alcotest.run_with_args
- Each fuzz module now exports `let suite = ("name", [test_case ...])`
- Entry points (fuzz.ml) collect suites: `Crowbar.run "pkg" [Fuzz_X.suite]`
- Remove stale `add_test`/`suite` API, keep only `test_case`/`run`
- Remove `let run () = ()` from fuzz_common.ml files
- Update merlint E725 rule to match new `let suite = ("name", ...)` pattern
- Update E725 test fixtures and expected output

- Restore cursor on exit via at_exit in Tty.Progress (fixes TTY corruption)
- Install SIGINT handler in monopam test for clean Ctrl-C
- Add 2s per-iteration timeout and 2s total budget to crowbar
- Group crowbar alcotest output by module prefix ("mdns: foo" → group "mdns")
- Skip fuzz runtest in afl context (enabled_if <> profile afl)
- Add merlint E725: enforce "module: description" fuzz test name convention

Migrate Printf.sprintf to Fmt.str, Format.fprintf to Fmt.pf, and
Format.pp_print_string to Fmt.string across bundle, gpt, hap, homebrew,
jsonwt, matter, mbr, meross, paseto, precommit, publicsuffix, qemu,
retry, sdnv, slack, sle, space-packet, spake2, sqlite, squashfs, tar,
tc, tcf, tcpcl, tm, tomlt, tty, uslp, vlog, wal, wire, yamlrw, yamlt,
osrelease, space, xdge, and crypto test runner.

Extract helper functions to reduce long function lengths across cwt, jsonwt,
ltp, matter, mbr, json-logs, and initramfs. Remove redundant find_/make_
prefixes in discovery.ml. Extract nested rm closure to reduce nesting depth.

Remove make_/get_/find_ prefixes from 21 functions: find_invalid_char,
make_api, make_cookie, get_json, get_keychain_passphrase,
get_all_linkedin_cookies, get_linkedin_cookies, get_int, get_uint,
get_bytes, get_partition_info, make_new_partition, make_new_mbr,
get_u8, get_u16_le, get_u32_le, get_ok, and related callers.

Replace hand-written get/set helpers and explicit offset constants with
type-safe Wire.Codec definitions for MBR partition entries (16 bytes),
GPT partition entries (128 bytes), and GPT headers (92 bytes). Add Wire
roundtrip tests for all three structures.

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.

Seeds added for disk/archive format parsers:
- ocaml-gpt: signature (8B), header_only (100B)
- ocaml-mbr: header_only (512B), zeroes (512B valid MBR)
- ocaml-cpio: header (110B), valid_archive (248B)
- ocaml-squashfs: magic (4B), superblock (96B)
- ocaml-tar: header (512B), valid_entry (1.5KB)

All seeds kept small (<1KB where possible) for efficient AFL mutation.

Fixes:
- cpio: Validate namesize > 0 before String.sub (crash on malformed input)
- squashfs: Fix compression test to check roundtrip validity

- Calculate CHS values from LBA for partition records
- Handle large disk values with clamping to 1023,254,63

- mbr: Rename package from mbr-format to mbr
- gpt: Update to use mbr instead of mbr-format
- uniboot: Fix Slice.of_bytes ~last parameter, add () for Vlog.setup

- Update mbr_inspect, read_partition, write_partition, resize_partition
to use Mbr.of_string and Mbr.to_string instead of cstruct-based API
- Update gpt_inspect to use Gpt.of_string instead of cstruct-based API
- Remove cstruct dependency from bin/dune files

Replace `let ( let* ) = Result.bind` with `open Result.Syntax` across
multiple packages: x509, tls, requests, ca-certs, cpio, jsonwt, matter,
tar, spake2, crypto, gpt, mbr.

The stdlib Result.Syntax module provides the same let* operator.

- ocaml-gpt: Use Result.Syntax, add MBR integration, fuzz tests
- ocaml-mbr: Add fuzz tests, update .ocamlformat
- ocaml-matter: Use Result.Syntax in pase.ml
- ocaml-requests/h2: Use Result.Syntax in H/2 implementation
- ocaml-tm: Fix .ocamlformat version, apply formatting
- ocaml-x509: Use Result.Syntax in ASN.1 grammars and PKCS#12