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Merge pull request 'docs(agents): the plan to consolidate six repositories into two' (#29) from plan/consolidation into main
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# Consolidating six repositories into two
**Set by the human, 2026-09-13.** The end state is **two** repositories:
| repo | holds |
|---|---|
| **`Sylpheed`** | everything — the port, the RE corpus, every tool |
| **`Xenia-Canary`** (our fork) | the emulator and oracle, with our instrumentation |
Everything else is retired. This page is the ordered **how**, with a gate after
each phase, and a ledger of what was checked rather than assumed.
⚠️ **Most paths on this page do not resolve in this repository, on purpose.**
They name files in `xenia-rs`, `xex2tractor`, `xenia-canary` and the project
root — the things being moved *in*. A citation checker pointed at
`docs/agents/` will flag every one of them until the phases below are done, and
that is the correct reading: **each unresolved path here is work outstanding.**
📌 Two decisions from the human frame the whole plan:
> *"The emulator is dead and can be dropped altogether. But the DuckDB generator
> should still be a useful tool… We probably can move it into a standalone tool
> under Sylpheed."*
> *"xex2tractor was an early attempt and is long dead too… you may want to scan
> and compare the tools for anything that is in xex2tractor only."*
---
## Where things stand
| repo | server | local tree | tracked | disposition |
|---|---|---|---|---|
| **Sylpheed** | 598 MB | 33 GB | 131 MB / 1470 files | the target |
| **Xenia-Canary** | 71 MB | 20 GB | — | the keeper — ⚠️ **dirty** |
| Syplheed-Reborn | 103 MB | 1.4 GB | 100 MB / 787 files | ✅ absorbed → archive |
| Sylpheed-Godot | 0.4 MB | 99 MB | 0.3 MB / 39 files | ✅ absorbed → archive |
| xenia-rs | 9 MB | 1.2 GB | 61 MB | harvest the DB tool → archive |
| xex2tractor | 0.3 MB | *no clone* | — | harvest four things → archive |
`Sylpheed` has **two root commits** — `feat: initialise workspace` (2026-03-25,
Reborn's) and `scaffold the Godot port` (2026-08-28). Both histories were
grafted in, not copied, which is why the absorption checks below pass.
## The ledger — what was verified, and how
Nothing here is inference. Each row is a command that was run on 2026-09-13.
| claim | method | result |
|---|---|---|
| Reborn fully absorbed | all **21 remote + 8 local** branch tips vs `Sylpheed/main` | every one an ancestor |
| Sylpheed-Godot absorbed | both branch tips, + the root-commit graft | every one an ancestor |
| `agent-backups/` redundant | `git bundle list-heads`, 23 refs across 4 bundles | all present in Sylpheed |
| 3 unpushed `pi/*` branches redundant | `git patch-id --stable`, per commit | all 4 patches on `main` |
| nothing lives outside git | issues / PRs / releases / wikis, all six repos | **0** everywhere but Sylpheed |
| the DB tool is separable | `git grep "use xenia_cpu::"` in `xenia-analysis` | **three symbols** |
### 🔴 What the ledger found that a naive plan would have destroyed
1. **The F1 instrument exists in one place, uncommitted.** `xenia-canary` has two
dirty files — `hid/file/file_input_driver.h` (`--pad_file_repeat`) and
`app/xenia_main.cc` — plus **4 unpushed commits** on `sylpheed-re` and a
branch, `audit-handle-lifecycle-probes`, **contained in no remote at all**.
That patch is the instrument behind `REPEAT_DELAY`/`REPEAT_INTERVAL`, now
shipped in the port. Its own finding page says *"not yet upstreamed."*
2. **xenia-rs has 4 unpushed branches** — `iterate-4B/ui-perf`, `4C/jit`,
`4D/parallel`, `4E/native-threads`. Dropping the emulator is a decision;
dropping work that was never backed up is a different act.
3. **The tool is not on `master`.** `xenia-rs/master` last moved **2026-06-15**;
the DuckDB and disassembler work is on `origin/iterate-4A/apu-xma-stage1`
(**2026-09-10**, +22 commits). Extract from the default branch and you get a
three-month-old tool.
---
## Phase 0 — Secure the single-copy work ✅ **DONE**
**Before touching anything else.** One `git checkout` in `xenia-canary` ends the
reproducibility of a measurement that is already live in the port.
1. Commit `file_input_driver.h` + `xenia_main.cc` on `sylpheed-re`.
2. Push `sylpheed-re` (4 + 1 commits) and `audit-handle-lifecycle-probes`.
3. ~~Resolve the `third_party/DirectXShaderCompiler` submodule drift.~~
✅ **There is none.** `git submodule status` shows no `+`: the checked-out
commit matches the recorded one. The ` m` in `git status` is *nested*
submodule dirt — DXC's own `external/SPIRV-Headers` and `SPIRV-Tools` — which
is upstream's business and must not be committed here.
**Gate — and the first version of it was wrong.** It compared each local branch
to a remote **by SHA**, and reported seven safe branches as unpushed: a branch
that is an *ancestor* of a pushed branch is already preserved. A check that goes
red for something unactionable is the failure this repo keeps naming, so the
gate tests what it means — **reachability**:
```bash
git for-each-ref --format='%(refname:short)' refs/heads | while read b; do
s=$(git rev-parse "$b"); found=""
for r in $(git for-each-ref --format='%(refname:short)' refs/remotes); do
git merge-base --is-ancestor "$s" "$r" 2>/dev/null && { found=$r; break; }
done
[ -n "$found" ] || echo "🔴 $b NOT REACHABLE from any remote"
done
```
✅ **PASSED 2026-09-13** — `8e63a9542` commits the instrument; `sylpheed-re` and
`audit-handle-lifecycle-probes` pushed; all **14** local branches reachable.
## Phase 1 — Make the archive honest ✅ **DONE**
Push xenia-rs `iterate-4B/ui-perf`, `4C/jit`, `4D/parallel`, `4E/native-threads`.
They are being retired, not rescued. But a retired branch that was never pushed
is not retired — it is deleted, quietly, by someone who thought it was safe.
**Gate:** the same loop, run in every repo, prints nothing.
✅ **PASSED 2026-09-13** — all four pushed (32 / 52 / 56 / 59 commits ahead of
`master`). The loop is clean in all five repos **except** `pi/clippy`,
`pi/clippy-clean` and `pi/reauth3` in Sylpheed, which are unreachable by
ancestry and redundant by *patch-id* — the ledger's reason, and Phase 7's
disposal. The gate is right to flag them; they are the one case where the
answer lives outside it.
## Phase 2 — Harvest xex2tractor, then retire it ✅ **DONE (PR #30)**
Four things exist only there.
| take | why |
|---|---|
| **XEX2 devkit + XEX1 retail master keys** | `xenia-xex` hardcodes retail only; devkit is present but `#[allow(dead_code)]` and XEX1 is absent. xex2tractor tries all three in a validating loop. |
| ~~**`extract -r`**~~ | 🔴 **RUN, AND THE INFERENCE WAS WRONG** — see the gate below. Optional, and dangerous if it is ever mistaken for the `.pe`. |
| **`doc/xex2_format.md`** (39 KB) and **`doc/xbox360_exports.json`** (938 KB, 2,913 exports across xboxkrnl / xam / xbdm) | byte-identical to untracked loose copies in the project root. Tracked by **no repo**. |
| **`LICENSE`** (MIT) | Sylpheed has none. |
Leave everything else: `xenia-xex` is ahead on `resources.rs` (XDBF/XACH),
`pdata.rs`, `tls.rs`, basic zero-fill compression, and the analysis layer.
**Gate — ✅ RUN 2026-09-13, and it corrected this page in two directions.**
```
extract (xex2tractor, no -r) ✅ IDENTICAL to the project .pe
extract -r (xex2tractor) ❌ differs — 1,903 bytes over 273 runs
extract (xenia-rs, iterate-4A) ✅ IDENTICAL — and .xex.json identical too
```
**Right:** the `.pe` *is* an xex2tractor extract. Hash-for-hash.
**Wrong:** it was made **without** `-r`. The project's `.pe` is the plain
decrypted-and-decompressed image, imports **unresolved** — and `-r`'s 1,903
differing bytes sit in the import thunk region from `VA 0x82000600`.
🔴 **So the dependency this gate existed to protect does not exist.** This page
claimed *"drop this and the file every `.pe`-offset citation depends on can
never be rebuilt."* It can: **`xenia-rs extract`, the tool Phase 3 keeps,
reproduces it byte-for-byte** — along with the loose `.xex.json`, which turns out
to have come from xenia-rs, not xex2tractor.
⚠️ **And `-r` must never become the `.pe`.** It writes into the image, so a `.pe`
built with it would silently invalidate every byte-offset citation in
`docs/re/`. If resolved-import disassembly is ever wanted, it is a **separate
artifact under a different name**, never a replacement.
That leaves xex2tractor's unique list at three items, none urgent — the two
master keys, the two doc assets, and the licence. **The doc assets are now the
only reason to visit that repository.**
📌 Learned in passing: `iterate-4A` **builds clean** (`xenia-app`, one unused
variable warning), so Phase 3's source is not bit-rotted — and it needs
`libavutil-dev` and friends via `ffmpeg-sys-next`, dragged in by the emulator's
XMA audio. The standalone tool sheds a C library the CI image did not have.
## Phase 3 — Lift the DB tool out of the emulator ✅ **DONE (PR #32)**
From `origin/iterate-4A/apu-xma-stage1`, **never** from `master`.
```
xenia-analysis 10,658 db, vtables, jumptables, func, xref, rtti,
strings, xdbf, static_init, demangle, sql_views
disasm slice of cpu 3,681 disasm.rs + decoder.rs + opcode.rs (of 21,813)
xenia-xex 2,018 header, loader, lzx, pe, pdata, tls, resources
xenia-vfs 444 so it reads an ISO, not just a loose .xex
xenia-types 361
───────
≈17,200 of ~71,000
```
The coupling is exactly three symbols — `decoder::decode`, `disasm::DisasmItem`,
`disasm::format`. Interpreter, JIT, scheduler, VMX, block cache, reservations:
none of it is reachable from the generator.
`xenia-xex` declares `xenia-memory` and `xenia-types` as dependencies and has
**zero `use`** of either. Probably droppable — confirm by compiling, do not
assume.
Travelling with it: `zq.py`, `tests/db_schema_golden.rs`,
`tests/disasm_goldens.rs`, `examples/decode_table_check.rs`.
**Two corrections to make during the move, not after:**
* the CLI help says **"SQLite database"** in two places. It is **DuckDB**
(`duckdb = { workspace = true }`).
* `zq.py`'s documented escape hatch — *"the engine vtable / rdata is NOT in the
DB … read it from guest memory with `xenia-rs exec --dump-addr`"* — **dies with
the emulator.** Replace it with Canary's dump or a direct read of the `.pe` at
`VA − 0x82000000`, and say which, in the file.
**Gate — ✅ PASSED 2026-09-13.** Schema a **superset** (22 new tables, none
lost). `instructions` 1,865,751, `pdata_entries`, `imports`, `sections` and all
three `eh_*` identical to the row; most others slightly higher. Two tables drop
~1.8 M and it is not a loss — the xref delta is **entirely `ind_call`**
(everything else nets **+1,512**), and the new schema records why: **6,556 sites
`truncated=true` carrying 1,801,075 candidates** against 427 untruncated
producing 4,199 rows. The old database materialised a cross product.
## Phase 4 — Prune the captures, and give `docs/re/` the check `docs/port/` has ✅ **DONE (PR #33)**
**`docs/re/captures/` is 257 files / 117.6 MB, and it is not junk.** Measured:
```
193 (81.2 MB) cited by a docs/re page, or opened by a tool
64 (36.5 MB) referenced by nothing
```
🔴 **Two are test fixtures and `cargo test` opens them:**
```
crates/sylpheed-formats/tests/ui_paint_order_disc.rs → captures/title-screen-oracle.png
crates/sylpheed-formats/tests/unit_layout_disc.rs → captures/stage02-live-unit-definitions-deep.txt
```
Sixteen more tools under `tools/port/` and `tools/re-capture/` read from there.
**Do:**
1. ✅ **DONE — `tools/re/check-capture-citations`**, the mirror of
`tools/port/check-citations`, which has only ever checked `docs/port/*.md`.
It reports two classes — a capture nothing cites, and a page citing a capture
that was never committed. It needs a `--selftest` that plants one of each, or
it is not a check.
2. ✅ **DONE — and there was ~~**10**~~ ONE.** Eight of the ten were *directory*
references that resolve; one was sentence punctuation in the regex. The real
one, `live-submenu-unidentified.png`, had been **committed and then deleted**
on 2026-08-30 while the page kept citing it and kept making the claim it
backs. Restored, not de-linked.
3. ✅ **DONE — 46, not 64.** Two are opened by *filename* from
`screen_match.py`, and sixteen sit inside directories that pages cite as
directories. 30.7 MB out of the checkout.
⚠️ **An orphan is not automatically waste.** It may be evidence a page *should*
have cited, and the page is the thing that is wrong. Fix the citations before
deleting, or step 3 silently ratifies every omission in step 2.
📌 **Going forward the class that matters is not captures-vs-code:**
| | |
|---|---|
| **evidence** — a screenshot a finding points at | belongs beside the finding, as the convention says |
| **run output** — `.jsonl`, `.log`, `.csv` | the same class as xenia-rs's `audit-runs/`, which this plan drops |
The two `.jsonl` mission-state dumps alone are 4.3 MB, and one is an orphan.
## Phase 5 — Verify the invariant, then archive ⬜ **NOT STARTED**
For each of `Syplheed-Reborn`, `Sylpheed-Godot`, `xenia-rs`, `xex2tractor`:
re-run the containment check **at that moment** — not from this page's ledger,
which will be days old — then archive read-only on Gitea, and only then delete
the local clone.
**Archive before delete, and leave them archived.** The check proves the commits
are reachable. It does not prove nobody will want the repository boundary back.
### ⚠️ The fork: history rewrite, or not
Dropping files in Phase 4 **reclaims no space**. The 118 MB is in history — 512
distinct blobs, 120.5 MB — and `git rm` leaves every byte in `.git` (590 MB
local, 598 MB on the server). Only a rewrite reclaims it, and it has a hard
blocker:
```toml
# crates/sylpheed-export/Cargo.toml:84
sylpheed-formats = { git = "…/Sylpheed.git", tag = "formats-pin-2026-09-01" }
```
**The build depends on this repo by tag**, pinned in `Cargo.lock` to `#1cd5b8b1`.
A rewrite invalidates all 8 `formats-pin-*` tags, every commit SHA, PR #23's
merge, both agents' clones, and needs a force-push through branch protection.
* **Don't rewrite** (recommended): 118 MB on a host with 154 GB free, where
`Sylpheed/target` alone is 32 GB. The cost is not worth the blast radius.
* **Do rewrite:** then it happens **here, in Phase 5** — while tags are being
re-cut and agents re-cloned anyway, so the disruption is paid once instead of
twice. Re-point the `formats-pin` dependency **first**.
This is a decision, not a default. Whichever is chosen, record it here.
## Phase 6 — Adopt the orphan assets ✅ **DONE (PR #34)**
Tracked by nobody today, and tools or references by the two-repo rule:
| asset | → |
|---|---|
| `ppc-manual/` — 397 files, **including `generator/generate_manual.py`** | Sylpheed |
| `docs/ppc_instructions.{json,md}`, `docs/xbox360_exports.*`, `docs/xex2_format.md` | Sylpheed `docs/` |
| `docs/CROSS_BUILD_SETUP.md` (58 KB) | **Canary** — it builds Canary |
| `run-canary.sh` | Sylpheed `tools/` |
| `ai-agent-*.md` ×4 (56 KB) | Sylpheed `docs/`, or discard — human's call |
| `scratch/xbg7/extract.py` — clean-room XBG7 scanner | superseded by `sylpheed_formats::mesh`; keep as history or drop |
| `Sylpheed-try/…/examples/_voice_span.rs` — 46-line untracked probe | keep or drop |
## Phase 7 — Intended drops ⬜ **NOT STARTED**
Stated so that nothing is dropped by omission.
| drop | size | why it is safe |
|---|---|---|
| `agent-backups/` | 687 MB | all 23 refs verified present in Sylpheed |
| `stock-oracle/` | 34 MB | two Canary **binaries**, rebuildable from source |
| root `canary_*.log` / `.stdout` / `.stderr` | ~15 MB | run output |
| `vkd3d-proton.cache` | 15 KB | runtime cache |
| xenia-rs `audit-runs/` | 57 MB, 41 files | already `.gitignore`d; `iterate-4A` deleted 40 of 41 |
| local `pi/clippy`, `pi/clippy-clean`, `pi/reauth3` | — | all 4 patches on `main`, by patch-id |
| `Sylpheed/target/` | **32 GB** | build output; the host is at 83 % |
| `texcompare/` (14 MB), `ship_render/` (64 KB) | — | tool output — **confirm no `docs/re/` page cites them first** |
| **the xenia-rs emulator** | ~54k LOC | the human's decision: superseded by Canary |
---
# ▶️ STATUS 2026-09-13 — paused here, for the other machine to finish
**Six of eight phases are done and pushed.** Everything below is committed;
nothing is left in a working tree. Five pull requests are open and **none has
been merged** — merging is the human's, and #32 contains #30 and #31.
| phase | state | where |
|---|---|---|
| **0** secure single-copy work | ✅ done | Canary `8e63a9542`, `sylpheed-re` + `audit-handle-lifecycle-probes` pushed |
| **1** make the archive honest | ✅ done | xenia-rs `iterate-4B/4C/4D/4E` pushed (32/52/56/59 commits) |
| **2** harvest xex2tractor | ✅ done | **PR #30** `harvest/xex2tractor-assets` |
| **3** lift the DB tool | ✅ done | **PR #32** `feat/xexdb-tool` |
| **4** captures + the missing check | ✅ done | **PR #33** `fix/capture-citations` |
| **6** adopt the orphan assets | ✅ done | **PR #34** `chore/adopt-orphan-assets`, + Canary `99cc72662` |
| — containers and agents | ✅ done | **PR #31** `docs/containers-setup` |
| **5** archive the four repos | ⬜ **open — needs the human** | |
| **7** intended drops | ⬜ **open — partly needs the human** | |
## 🔴 Four claims on this page were wrong. Read these before trusting the rest.
1. **"10 dangling citations" was ONE.** Eight were *directory* references, which
resolve and are simply absent from `git ls-tree`; one was a path at the end of
a sentence with the full stop pulled into the match. The figure is corrected
in Phase 4 below and in PR #33.
2. **`extract -r` is not how the `.pe` was made**, and nothing depends on it —
Phase 2's gate, run.
3. **The Phase 0 gate compared branches by SHA** and called seven safe branches
unpushed. It tests reachability now.
4. **There is no DXC submodule drift.** The ` m` is *nested* submodule dirt.
## What the other machine should do next
### Before anything: merge or decide on the open PRs
```
#30 harvest/xex2tractor-assets reference files + LICENSE
#31 docs/containers-setup container and agent setup
#32 feat/xexdb-tool the DuckDB tool ⚠️ CONTAINS #30 and #31
#33 fix/capture-citations the docs/re check + prune
#34 chore/adopt-orphan-assets PPC manual + canary launcher
```
⚠️ **#32 is stacked.** Merge #30 and #31 first, or merge #32 and close them —
its `build.rs` needs #30's export table, so they cannot be independent.
⏳ **One result outstanding:** the workspace `cargo test` count for #32. `check`,
`clippy`, `fmt` and `wasm` are all 0; the test leg was interrupted twice by
branch switches and never reported cleanly. Run it and post the number:
```bash
docker/ci/run cargo test --workspace
```
### Phase 5 — archive, and the history fork
**Do not trust this page's ledger when you get there.** Re-run the containment
check *at that moment* — days will have passed and branches may have moved:
```bash
for repo in Syplheed-Reborn Sylpheed-Godot xenia-rs xex2tractor; do
# every ref of $repo must be an ancestor of a Sylpheed ref
done
```
Then **archive read-only on Gitea**. 🔴 **Do not delete any repository.** Archiving
is reversible; deletion is not, and it is the human's call, separately, later.
Nothing outside git needs migrating — issues, PRs, releases and wikis are **zero**
in all four (verified).
The **history-rewrite fork** is still open and still recommended AGAINST: the
118 MB is in history, and `crates/sylpheed-export/Cargo.toml` depends on this
repo **by tag** (`formats-pin-2026-09-01`, pinned in `Cargo.lock`). A rewrite
invalidates all 8 tags, every SHA, PR #23's merge and both agents' clones.
### Phase 7 — the drops
All verified, none done — they are deletions on the human's disk:
```
agent-backups/ 687 MB 23 refs verified present in Sylpheed
Sylpheed/target/ 32 GB build output; the host is at 83 %
stock-oracle/ 34 MB two Canary binaries, rebuildable
root canary_*.log 15 MB run output
xenia-rs audit-runs/ 57 MB already .gitignore'd; iterate-4A deleted 40 of 41
pi/clippy, pi/clippy-clean, pi/reauth3 all 4 patches on main, by patch-id
texcompare/ (14 MB), ship_render/ confirm no docs/re/ page cites them first
```
### Still the human's, untouched
`ai-agent-*.md` ×4 (56 KB), `scratch/xbg7/extract.py`, `_voice_span.rs`, and the
**retention question**: all six repos are `private=False`, and `docs/re/captures/`
is ~87 MB of game screenshots in a public repository.
## What each finished phase actually produced
* **Phase 2** — `docs/reference/{xex2-format.md, xbox360-exports.*, ppc-instructions.*}`
and an MIT `LICENSE`; this repo had none. The first two are byte-identical to
xex2tractor's, verified with `cmp`.
* **Phase 3** — `sylpheed-xex` + `sylpheed-ppc` + `sylpheed-xexdb`, ≈17,200 lines
of ~71,000, coupled to the emulator by **three symbols**. The gate: a
regenerated database whose schema is a superset, with `instructions`,
`pdata_entries`, `imports`, `sections` and `eh_*` identical to the row. The two
−1.8 M deltas are the `max_indirect_candidates` ceiling, recorded by the tool
as **6,556 truncated sites standing for 1,801,075 candidates** — checked, not
assumed: the xref delta is entirely `ind_call`. `build.rs` no longer reads a
sibling checkout, and a missing export table now **fails** instead of silently
producing a database with no import names.
* **Phase 4** — `tools/re/check-capture-citations`, 212 captures all cited, 46
orphans dropped. It caught its own damage twice: two "orphans" are opened by
*filename* from `screen_match.py`, and the first prune emptied two directories
that pages cite *as directories*.
* **Phase 6** — `tools/ppc-manual/` (393 files) and a rewritten
`tools/run-canary.sh`; the old one pointed at a **symlink** Wine cannot resolve
and hardcoded one machine's paths. The full `CROSS_BUILD_SETUP.md` went to
Canary, where the tracked copy was a 6.8 KB stub of a 59 KB guide.
## The method, if you only read one thing
Every claim on this page that was *reasoned* turned out wrong, and every one that
was *run* held. The gates are the point: Phase 2's gate refuted its own premise,
Phase 3's proved the two alarming row deltas were an improvement, and Phase 4's
check caught a deletion I had just made. **Run them again rather than trusting
the results recorded here.**
## Still open, for the human
* **Retention.** The `.iso` (7.6 GB), `.pe`, `.xex.json` and `sylph_extract/`
(6.2 GB) stay on disk and out of git. But `docs/re/captures/` is 118 MB of
game screenshots **inside a public repository**, about to be joined by a
938 KB export database, and **all six repos are `private=False`**. Worth
choosing rather than inheriting.
* **The history fork** in Phase 5.
* **`ai-agent-*.md`, `scratch/`, `_voice_span.rs`** — keep or drop.