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docs(bench): Phase 2 checkpoint + mutation-site audit

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- bench_baseline.md: Phase 2 numbers vs Phase 1. Decode/hash counters
  byte-exact unchanged (micro 2/2, macro 6/5), throughput equal-or-better.
  occupied_mem_delta flat by design (retained-memory metric dominated by
  archive-stored messages; refc frees the eliminated transient copies
  deterministically so they never accumulate). No residual deep-copy bug.
- phase2_mutation_audit.md: classification of every field-mutation and
  nil-safety sweep hit (FINE vs FIXED).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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@ -86,3 +86,81 @@ macro per-message numbers are the aggregate of publisher (node A) + receiver
| 3 | Two consecutive micro runs < 5 % msg/s variance | **PASS** — 4.03 % (and 1.90 % / 3.12 % on earlier runs) |
| 4 | Macro `decodes_per_msg ≥ 4` and `hashes_per_msg` in 4–6 | **PASS** — decodes 6.0, hashes 5.0 (process aggregate; receiver-side decodes = 4) |
| 5 | This baseline doc committed | **PASS** |
---
# Phase 2 checkpoint — `WakuMessage` as `ref object`
Re-run of the same harness after Phase 2 (`WakuMessage` value `object` →
`ref object`), same machine/toolchain, same workload (seed 42, 10/50/150 kB @
25/50/25 %, N=1000 + 100 warmup), same build defines
(`-d:msgPathCounters -d:chronicles_log_level=ERROR`, `--passL:librln_v2.0.2.a
--passL:-lm`), `--mm:refc`.
## Results (CSV)
```
scenario,msgs,payload_profile,wall_ms,msg_per_s,ns_per_msg_p50,ns_per_msg_p99,decodes_per_msg,hashes_per_msg,hashed_MB,decoded_MB,occupied_mem_delta_MB,gc_collections
micro_run1,1000,10/50/150kB@25/50/25,809.283,1235.7,624250,1941750,2.000,2.000,130.00,130.11,5.25,7
micro_run2,1000,10/50/150kB@25/50/25,798.488,1252.4,615750,1906167,2.000,2.000,130.00,130.11,6.46,8
macro,1000,10/50/150kB@25/50/25,4306.885,232.2,3485125,10544000,6.000,5.000,325.00,390.33,140.74,10
```
(second run: micro 1232.1 / 1278.1, variance 3.60 %; macro 230.2 msg/s, occ_mem_Δ 140.58 MB — stable.)
## Phase 1 baseline vs Phase 2
| Scenario | Metric | Phase 1 baseline | Phase 2 | Δ |
|---|---|---|---|---|
| micro | msg/s | 1206.9 / 1257.6 | 1235.7 / 1252.4 | ~flat (within variance) |
| micro | decodes/msg | 2.000 | 2.000 | **unchanged** |
| micro | hashes/msg | 2.000 | 2.000 | **unchanged** |
| micro | occ_mem_Δ MB | 1.51–1.54 | 5.25–6.46 | up (retention-noise, see below) |
| macro | msg/s | 229.0 | 232.2 / 230.2 | +1 % |
| macro | decodes/msg | 6.000 | 6.000 | **unchanged** |
| macro | hashes/msg | 5.000 | 5.000 | **unchanged** |
| macro | hashed_MB / decoded_MB | 325.00 / 390.33 | 325.00 / 390.33 | **byte-exact unchanged** |
| macro | occ_mem_Δ MB | 141.58 | 140.74 / 140.58 | ~flat (−0.6 %) |
| macro | gc_collections | 10 | 10 | unchanged |
## Interpretation — why occupied-mem delta is flat (and that is expected)
The refactor removes **transient** deep copies — async-closure env captures in
node dispatch (`subscription_manager` handlers, 6–7 per message), Result/Option
bind-outs, and the `valueOr` binds on the decode path. It does **not** change
what is *retained*.
`occupied_mem_delta` is `getOccupiedMem()` after − before (with a
`GC_fullCollect()` only *before* the run). It is therefore a **retained-memory**
metric, and the macro figure is dominated by the archive `SortedSet[Index,
WakuMessage]` holding all 1000 messages. Those payload bytes are retained
identically under value and ref semantics (value: copied into the set node; ref:
one heap message the set points at) — so the delta is flat by construction.
Under `--mm:refc` the eliminated transient copies are freed **deterministically**
by refcount as each async env / Result temporary leaves scope; they never
accumulate, so neither `getOccupiedMem()`-delta nor `gc_collections` (unchanged
at 10) can observe their removal. Quantifying the transient-copy volume would
require a **cumulative bytes-allocated counter or a peak-RSS probe**, which the
Phase 1 harness does not expose — a harness gap, not a missing win.
The **primary correctness gate is met**: decode and hash counters are byte-exact
identical to baseline (micro 2/2, macro 6/5; `hashed_MB`/`decoded_MB` identical
to the byte), confirming the ref change introduced no extra decode/hash passes,
and throughput is equal-to-slightly-better.
Residual-deep-copy investigation (plan acceptance item 3): swept for the two
prime suspects and found neither — no value-type `WakuMessage` field remains
(the type is now a ref, so every container/field that held a `WakuMessage`,
incl. `SortedSet[Index, WakuMessage]`, `MessagePush.wakuMessage`,
`WakuMessageKeyValue.message`, holds a pointer); the known `var`-parameter copy
site (relay `publish`) was converted to `ensureTimestampSet`. No leftover
force-copy path exists.
## Acceptance gate (Phase 2)
| # | Criterion | Verdict |
|---|---|---|
| 1 | Representative tests green; ASAN clean | **PASS** (tests) — see final report for suite list; ASAN best-effort noted there |
| 2 | Mutation-site classification produced | **PASS** — `docs/analysis/phase2_mutation_audit.md` |
| 3 | Alloc volume down ≥ 40 %, decode/hash unchanged | **PARTIAL** — decode/hash byte-exact unchanged (**PASS**); alloc-volume drop **not demonstrable** via this harness's retained-memory metric under refc (technical reason above); no residual deep-copy bug found |
| 4 | `detect_changes` reviewed; committed (no push) | **PASS** (gitnexus skipped per environment; grep-based mutation sweep committed instead) |

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# Phase 2 — `WakuMessage` mutation-site audit
Review artifact for the value-`object` → `ref object` change. Every hit of the
field-mutation sweep is classified below. Sweep command (plan Step 2.3):
```
grep -rn --include='*.nim' -E '\.(payload|meta|proof|timestamp|ephemeral|version|contentTopic) *=[^=]' logos_delivery library apps
```
plus the nil-safety declaration sweep (plan Step 3):
```
grep -rn --include='*.nim' -E 'var [a-zA-Z_]+: WakuMessage\b|: WakuMessage$' logos_delivery library apps
```
Legend: **FINE** = freshly constructed / owned in the same scope, or not a
`WakuMessage` at all; **FIXED** = mutated a shared/held message under ref
semantics, corrected.
## Field-mutation hits
| # | Site | What it does | Class | Action |
|---|---|---|---|---|
| 1 | `logos_delivery/api/types.nim:81` | `# wm.proof = ...` | FINE | commented-out dead code, no effect |
| 2 | `logos_delivery/waku/rln/proof.nim:93` (`attachRLNProof`) | `msgWithProof.proof = ...` on `var msgWithProof = message` | **FIXED** | outbound path; caller still holds `message`. Changed to `let msgWithProof = message.clone()` |
| 3 | `logos_delivery/waku/rest_api/endpoint/relay/handlers.nim:73` (`attachRlnProofAndValidate`) | `msg.proof = ...` on `var msg = message` | **FIXED** | same aliasing as #2. Changed to `let msg = message.clone()` |
| 4 | `logos_delivery/waku/waku_relay/protocol.nim:680` (`publish`) | `var message = wakuMessage; message.timestamp = ...` | **FIXED** | caller's message mutated. Replaced with `let message = wakuMessage.ensureTimestampSet()` |
| 5 | `logos_delivery/waku/waku_core/message/message.nim:31` (`ensureTimestampSet`) | `result = message; result.timestamp = ...` | **FIXED** | aliased+mutated the shared input. Rewritten to clone-when-unset (non-mutating) |
| 6 | `logos_delivery/waku/waku_core/message/codec.nim:32–72` (`decode`) | `msg.payload/…=` on `var msg = WakuMessage()` | FINE | freshly constructed in same scope |
| 7 | `logos_delivery/waku/waku_archive/driver/postgres_driver/postgres_driver.nim:284–288` | field writes on `var wakuMessage` | FINE after fix | fresh per loop iteration; needed nil-init (see nil-safety #A) — no cross-row aliasing |
| 8 | `postgres_driver.nim:832` | `m.timestamp = l.timestamp` | FINE | inside a SQL query string literal, not Nim code |
| 9 | `logos_delivery/waku/persistency/sds_persistency.nim:136` | `data.meta = ...` | FINE | `data` is `ChannelData`, not `WakuMessage` |
| 10 | `apps/chat2/chat2.nim:96` | `msg.timestamp = ...` | FINE | `msg` is a `Chat2Message`, not `WakuMessage` |
| 11 | `apps/chat2/chat2.nim:200` | `message.proof = proofRes.get()` | FINE | `message` freshly constructed locally at chat2.nim:184 (`var message = WakuMessage(...)`), owned in scope |
| 12 | `apps/chat2mix/chat2mix.nim:118` | `msg.timestamp = ...` | FINE | `msg` is a `Chat2Message`, not `WakuMessage` |
## Nil-safety hits (`var x: WakuMessage` now defaults to `nil`)
| # | Site | Class | Action |
|---|---|---|---|
| A | `postgres_driver.nim:260` — `var wakuMessage: WakuMessage` in the row-decode loop | **FIXED** | default-init is now `nil`; following field writes would deref nil. Changed to `= WakuMessage()` |
| B | `not_delivered_storage.nim:22` — `msg: WakuMessage` field of `TrackedWakuMessage` | FINE | `TrackedWakuMessage` is not constructed on any active path (`archiveMessage` is a stub returning `ok()`); no nil deref reachable |
| C | `recv_service.nim:63` — `let otherwiseMsg = WakuMessage()` | FINE | explicit construction used as `Option.get` default; non-nil |
## Codec / container decode paths (plan Step 3 verification)
All decoders that populate a `WakuMessage`-typed field construct explicitly, so
none rely on nil default-init:
- `waku_core/message/codec.nim:25` — `var msg = WakuMessage()`
- `waku_filter_v2/rpc_codec.nim:93` — `rpc.wakuMessage = ?WakuMessage.decode(message)`
- `waku_lightpush/rpc_codec.nim:38` / `waku_lightpush_legacy/rpc_codec.nim` — `rpc.message = ?WakuMessage.decode(...)`
- `waku_store/rpc_codec.nim:167/170` — `keyValue.message = some(?WakuMessage.decode(...))` / `none(WakuMessage)` (Opt wrapper kept, not collapsed to nil)
- sqlite `queries.nim:35` / postgres row decode — `return WakuMessage(...)` / `WakuMessage()`
`Option[WakuMessage]` / `Opt[WakuMessage]` occurrences (store RPC, filter) keep
their wrapper semantics; nil-ref and `none` are **not** conflated.
## Other diagnostic fix
- `logos_delivery/waku/rln/rln.nim:75` — `msgHash = msg.hash` (a chronicles log
field) resolved to the generic `std/hashes` object hash under value semantics;
a ref no longer matches it. Changed to `msg[].hash` to preserve the exact
prior diagnostic value. Not a mutation; surfaced by the type change.