Follow-ups: ledger_merge.py sync, two environment-proof test fixes, 6 intake prompts

REFERENCE.md

@@ -823,6 +823,15 @@ What blocks, and what does not:
   sides changed differently is the only conflict — takes `main`'s copy of the
   renders, and leaves `autonomy_log.md` to git's `merge=union` driver
   (`.gitattributes`; it is append-only). What that cannot settle blocks.
+- **Branches the workflow never touches sync locally the same way.** A session
+  branch (`ccr-*` and the like) or a PR branch holding code must catch up with
+  `main` by hand, and its generated files conflict on almost every concurrent
+  push. `git fetch origin main && python3 scripts/ledger_merge.py sync` runs the
+  same merge: `--no-commit` merge of `origin/main`, `resolve`, then
+  `complete/index.md` and the dashboard re-rendered on the merged tree (the
+  Brain renderer from `$PYAUTO_BRAIN` or a sibling `PyAutoBrain`), staged for
+  you to commit. It refuses a dirty tree and stops, merge in progress, on
+  anything the grammar cannot settle.
 - **A blocked branch is written on an issue** titled ``ledger merge: `<branch>`
   needs a human`` (label `ledger-merge`), updated on every further attempt and
   closed by the run that finally lands it. A red run nobody is subscribed to

complete/2026/11/bootstrap-test-root-skip.md

@@ -0,0 +1,30 @@
+- summary: fixed in commit 748f8c0bb (this PR). `test_the_hook_survives_an_unwritable_tools_dir` probes `os.access(bin, W_OK)` after the chmod and skips with "cannot make a directory unwritable here (running as root?)" when root ignores the mode bits. As a normal user it still drives the failure path.
+- witness: in this cloud container (root), `pytest tests/test_session_bootstrap.py -rs` reports 1 skipped with that reason. Mind suite 728 passed, 1 skipped.
+
+## Original prompt
+
+# `test_the_hook_survives_an_unwritable_tools_dir` fails when the suite runs as root
+
+Type: bug
+Target: PyAutoMind
+Repos:
+- PyAutoMind
+Themes:
+- ci
+Difficulty: small
+Autonomy: safe
+Priority: low
+Status: formalised
+Filed: 2026-11-05
+Consequence: glance
+Witness: `pytest tests/test_session_bootstrap.py` reports the test as SKIPPED with a reason when run as root (cloud containers) and still drives the failure path as a normal user.
+Review-minutes: 2
+Unattended: ready
+
+The test chmods a tool env's `bin/` to 0o500 to force `repair_uv_tools` down its "could not
+repoint" path. Root ignores mode bits, so in a cloud session (tests run as root) the path is never
+taken and the test fails on the environment, not on the code. Every Mind suite run in the
+2026-11-05 queue session reported it as a known failure. Fix: probe `os.access(..., W_OK)` after
+the chmod and skip with a reason when the directory is still writable.
+
+<!-- formalised by the Intake (Conception) Agent on 2026-11-05 from file:/tmp/claude-0/-home-user/ad8c6486-73f7-504b-b742-a7b629366ade/scratchpad/intake/a_bootstrap_root.md -->

complete/2026/11/ledger-merge-sync.md

@@ -0,0 +1,36 @@
+- summary: shipped in commit 748f8c0bb (this PR). `scripts/ledger_merge.py sync [--base origin/main] [--root]` / `sync_with_base()` does what `mind_ledger_merge.yml` does, for branches it never touches. It refuses a dirty tree; runs `git merge --no-commit --no-ff <base>`; uses `resolve_conflicts` (registries merge by entry, renders conflict-free); stops as `blocked` with the merge in progress on anything the grammar cannot settle; otherwise re-renders `complete/index.md` (`lifecycle.py index --apply`) and the dashboard (the Brain renderer from `$PYAUTO_BRAIN` or a sibling/organs `PyAutoBrain`, else a NOT-regenerated note) on the merged tree; and stages them for the caller to commit. Documented in REFERENCE.md "How the ledger lands".
+- witness: 3 new tests in tests/test_ledger_merge.py: ready + entry merge + injected re-render + MERGE_HEAD staged; up-to-date no-op and dirty-tree refusal; a non-ledger conflict blocked before rendering. 31 passed in that file.
+- not done: extending the auto-merge workflow to `ccr-*` session branches. That is a policy decision for the human.
+
+## Original prompt
+
+# `ledger_merge.py sync`: bring a non-`claude/**` Mind branch up to date with main…
+
+Type: feature
+Target: PyAutoMind
+Repos:
+- PyAutoMind
+Themes:
+- mind-workflow
+Difficulty: small
+Autonomy: supervised
+Priority: medium
+Status: formalised
+Filed: 2026-11-05
+Consequence: judge
+Witness: tests drive a fixture repo — a session branch behind main with entry-level registry changes on both sides and conflicting renders — through `sync_with_base`: status `ready`, registries merged by entry, renders regenerated on the merged tree by the (injected) renderer, merge left staged; `up-to-date` is a no-op; a dirty tree is refused; a non-ledger conflict stops as `blocked` before rendering.
+Review-minutes: 5
+Unattended: ready
+
+`mind_ledger_merge.yml` settles concurrent-push conflicts for `claude/**`, `codex/**` and
+`chatgpt/**` branches (`ledger_merge.py resolve`, then re-render). Session branches (`ccr-*`) and
+PR branches holding code get none of that: PyAutoMind#539 needed three rounds of hand conflict
+resolution on `dashboard.md` / `dashboard.html` / `state.json` / `complete/index.md` as other
+sessions pushed to main every few minutes, and one round kept main's stale index because the
+manual regen was a dry run (red `drift` check). A `.gitattributes` merge driver does not help:
+GitHub ignores custom drivers. Add `ledger_merge.py sync [--base origin/main]` — merge with
+`--no-commit`, `resolve`, re-render the generated files on the merged tree, stage, let the caller
+commit — and document it beside the workflow in REFERENCE.md "How the ledger lands".
+Extending the auto-merge workflow to `ccr-*` branches is a separate policy decision (not here).
+
+<!-- formalised by the Intake (Conception) Agent on 2026-11-05 from file:/tmp/claude-0/-home-user/ad8c6486-73f7-504b-b742-a7b629366ade/scratchpad/intake/c_sync.md -->

complete/2026/11/root-default-test-env-leak.md

@@ -0,0 +1,30 @@
+- summary: fixed in commit 748f8c0bb (this PR). The module's autouse `forget_the_resolver` fixture now deletes `PYAUTO_ROOT` and `PYAUTO_ROOT_REASON` via monkeypatch. `test_an_explicit_override_is_never_second_guessed` still sets its own value.
+- witness: `PYAUTO_ROOT=/home/user pytest tests/test_repos_sync_root_default.py` passes. The full suite gives 728 passed, 1 skipped, with and without the variable exported.
+
+## Original prompt
+
+# `test_repos_sync_root_default` inherits an exported `PYAUTO_ROOT` and fails
+
+Type: bug
+Target: PyAutoMind
+Repos:
+- PyAutoMind
+Themes:
+- ci
+Difficulty: small
+Autonomy: safe
+Priority: low
+Status: formalised
+Filed: 2026-11-05
+Consequence: glance
+Witness: `PYAUTO_ROOT=/somewhere pytest tests/test_repos_sync_root_default.py` passes.
+Review-minutes: 2
+Unattended: ready
+
+`workspace_root()` treats an exported `PYAUTO_ROOT` as "the operator's word" and never second-
+guesses it, so `test_a_root_that_does_not_hold_this_checkout_is_refused` fails whenever the shell
+running the suite has it exported — which the Brain CLI does for its children (observed
+2026-11-05 after a `pyauto-brain intake` run in the same shell). Fix: the module's autouse fixture
+clears `PYAUTO_ROOT` / `PYAUTO_ROOT_REASON` via monkeypatch; the override test sets its own.
+
+<!-- formalised by the Intake (Conception) Agent on 2026-11-05 from file:/tmp/claude-0/-home-user/ad8c6486-73f7-504b-b742-a7b629366ade/scratchpad/intake/b_root_env_leak.md -->

complete/index.md

@@ -6,7 +6,7 @@ Token-light navigation over the finished-work records (schema:
 only then grep a dated bucket. Curators: edit the band between the CURATED
 markers; everything below GENERATED is rebuilt.
 
-2172 records across 11 buckets.
+2175 records across 11 buckets.
 
 <!-- CURATED:START -->
 ## Highlights
@@ -136,6 +136,7 @@ markers; everything below GENERATED is rebuilt.
 - [autonomous-orchestrators-p4b](2026/11/autonomous-orchestrators-p4b.md) — phase 4b of 4a–4c; epic draft/feature/pyautobrain/autonomous_orchestrators_epic.md
 - [batch-watch-live-view](2026/11/batch-watch-live-view.md) — pilot 4c follow-up; issue PyAutoBrain#575
 - [board-without-gh-phase2-legs](2026/11/board-without-gh-phase2-legs.md) — already shipped, closed as a stale draft. PyAutoBrain 15317af (merged via #564, 2026-11-03) "phase 2 — the rem…
+- [bootstrap-test-root-skip](2026/11/bootstrap-test-root-skip.md) — fixed in commit 748f8c0bb (this PR). `test_the_hook_survives_an_unwritable_tools_dir` probes `os.access(bin, W…
 - [brain-hygiene-cleanup-bugs](2026/11/brain-hygiene-cleanup-bugs.md)
 - [chapter2-continuation](2026/11/chapter2-continuation.md) — All continuation scope merged: Tutorials 5 and 6, optional speed and runnable model_centred prior passing, sum…
 - [cloud-validation-rehearsal-clock-skew](2026/11/cloud-validation-rehearsal-clock-skew.md)
@@ -168,6 +169,7 @@ markers; everything below GENERATED is rebuilt.
 - [intake-memory-line-organ-targets](2026/11/intake-memory-line-organ-targets.md) — already shipped — closed as stale draft. The `_with_memory` gate in `agents/conductors/intake/_intake.py` land…
 - [jax-joss-benchmark-repo](2026/11/jax-joss-benchmark-repo.md) — already shipped — PyAutoLabs/autolens_jax_joss: 9c66b020 (birth, 10 benchmark scripts), 64204f69 (A100 sweep o…
 - [latest-per-test-tie](2026/11/latest-per-test-tie.md) — test_autofit/results/test_identity.py::test_latest_per_keeps_the_latest_sibling flaked (main red at 963ff296a,
+- [ledger-merge-sync](2026/11/ledger-merge-sync.md) — shipped in commit 748f8c0bb (this PR). `scripts/ledger_merge.py sync [--base origin/main] [--root]` / `sync_wi…
 - [lifecycle-p3-designation-proposals](2026/11/lifecycle-p3-designation-proposals.md) — decided and shipped — the human approved all 39 designations (datacube/delaunay gpu_a100 held provisional); Py…
 - [likelihood-lifecycle-p3-day-zero-pages](2026/11/likelihood-lifecycle-p3-day-zero-pages.md)
 - [likelihood-lifecycle-p3-day-zero-stamp](2026/11/likelihood-lifecycle-p3-day-zero-stamp.md)
@@ -204,6 +206,7 @@ markers; everything below GENERATED is rebuilt.
 - [results-library-p3-exports](2026/11/results-library-p3-exports.md) — phase 3; ledger draft/feature/autofit/results_library_epic.md
 - [results-library-p4-package](2026/11/results-library-p4-package.md) — phase 4; ledger draft/feature/autofit/results_library_epic.md
 - [results-library-p5b-cortex](2026/11/results-library-p5b-cortex.md) — phase 5b; ledger draft/feature/autofit/results_library_epic.md
+- [root-default-test-env-leak](2026/11/root-default-test-env-leak.md) — fixed in commit 748f8c0bb (this PR). The module's autouse `forget_the_resolver` fixture now deletes `PYAUTO_RO…
 - [rtd-organism-currency](2026/11/rtd-organism-currency.md) — already shipped, closed as a stale draft. PyAutoBrain 1aa2ed4 (#563) renamed `docs/organs/build` to `organs/ha…
 - [scientist-minimal-starter](2026/11/scientist-minimal-starter.md) — already shipped — Mind#502 / PR #503, record `complete/2026/10/scientist-starter-acceptance.md`; slices PyAuto…
 - [search-seed-reproducibility](2026/11/search-seed-reproducibility.md) — already shipped — PyAutoFit#1686 (5bf057f2, 2026-10-14; search-ext A4b), record `complete/2026/10/search-ext-a…