chore: rename current-facing PyAutoConf → PyAutoNerves refs

.github/workflows/morning_status.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       REPOS: >-
-        PyAutoLabs/PyAutoConf
+        PyAutoLabs/PyAutoNerves
         PyAutoLabs/PyAutoFit
         PyAutoLabs/PyAutoArray
         PyAutoLabs/PyAutoGalaxy

AGENTS.md

@@ -7,7 +7,7 @@ this repository.
 
 **PyAutoMind is the Mind of the PyAuto organism and the starting point of the
 PyAuto workflow.** It holds the organism's ideas, intent, goals, priorities and
-workflow state. Every task that ends up as a PR in PyAutoConf, PyAutoFit,
+workflow state. Every task that ends up as a PR in PyAutoNerves, PyAutoFit,
 PyAutoArray, PyAutoGalaxy, PyAutoLens, or any of the `*_workspace*` repos begins
 as a markdown file here.
 

docs/pyautobrain/pyautoscientist_phase3_research.md

@@ -5,7 +5,7 @@ Research note, 2026-07-10. Companion to `pyautoscientist_generalisation_assessme
 discussion: the maintainer's vision is **more rigid** than the shipped docs'
 category contract — a literal `PyAutoProject` / `autoproject_workspace` /
 `autoproject_workspace_test` / `autoproject_assistant` family a new scientist
-adopts wholesale, with PyAutoConf promoted to the organism's "nervous system".
+adopts wholesale, with PyAutoNerves promoted to the organism's "nervous system".
 Constraints unchanged: no duplicated code, no impact on the live setup, and
 the live organs stay the single fast-moving upstream adopters tag along with.
 
@@ -26,7 +26,7 @@ a satellite must follow:
 | Config layering (packaged defaults ← workspace override) | the `autoconf` package at runtime | a `config/` directory in the documented shape |
 
 **The one gap:** `smoke_tests.yml` is a fat per-workspace copy (hard-coded
-checkout chain of PyAutoConf → … → the library) in every workspace and HowTo —
+checkout chain of PyAutoNerves → … → the library) in every workspace and HowTo —
 ~10 near-identical files in the live setup. Generalising it into a reusable
 workflow parameterised by the dependency chain is a Phase 3 work item that
 pays the live setup directly (one definition instead of ten) *and* is the
@@ -113,9 +113,9 @@ one generator maintains every fresh-slate artifact against the live source
 of truth. Drift check: a CI job re-runs spawn and fails on diff — the
 repos_sync pattern, again.
 
-## 4. PyAutoConf → PyAutoNerves: promote the role now, defer the rename
+## 4. PyAutoNerves → PyAutoNerves: promote the role now, defer the rename
 
-PyAutoConf genuinely is the nervous system — the runtime layer connecting
+PyAutoNerves genuinely is the nervous system — the runtime layer connecting
 workspace conventions to libraries (layered config with workspace override,
 version handshake, test_mode, jax_wrapper, notebook/Colab setup). The
 adopter-facing framing "your project gets `autoproject/config/` +
@@ -126,7 +126,7 @@ But the literal rename decomposes into three moves with very different costs:
 
 1. **Promote the role** — body map `role:` text, an RTD "Nerves" page beside
    the organ pages, template family wired through it. Zero risk. **Do now.**
-2. **Rename the repo** (PyAutoConf → PyAutoNerves, keep package `autoconf`)
+2. **Rename the repo** (PyAutoNerves → PyAutoNerves, keep package `autoconf`)
    — GitHub redirects help, but the name is hard-coded in every fat
    `smoke_tests.yml` checkout, docs-build.yml's dep chains, Heart config,
    pre_build, repos.yaml + all generated blocks, and the firewall allowlist.

scripts/repos_sync.py

@@ -194,7 +194,7 @@ def system_map(categories, repos):
 
 def public_organs(repos):
     """The front-door organ set: every `category: organ` row (manifest order)
-    plus any repo flagged `front_door: true` (e.g. Nerves/PyAutoConf — a
+    plus any repo flagged `front_door: true` (e.g. Nerves/PyAutoNerves — a
     library that is part of the organism's public self-presentation without
     being a category:organ). This is a *superset* of the internal organism map
     (`system_map`, strict category:organ per PyAutoBrain/ORGANISM.md); the two
@@ -518,18 +518,18 @@ def write_claude_md_pointers(root, repos):
     "PyAutoBrain/agents/_common.sh": {"PyAutoLabs"},
     "PyAutoBrain/agents/conductors/bug/_bug.py": {"PyAutoArray"},
     "PyAutoBrain/agents/conductors/bug/bug.sh": {"PyAutoLabs"},
-    "PyAutoBrain/agents/conductors/health/health.sh": {"PyAutoConf"},
+    "PyAutoBrain/agents/conductors/health/health.sh": {"PyAutoNerves"},
     "PyAutoBrain/agents/conductors/hygiene/_hygiene_config.py": {"PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
-    "PyAutoBrain/agents/conductors/hygiene/hygiene.sh": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
+    "PyAutoBrain/agents/conductors/hygiene/hygiene.sh": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
     "PyAutoBrain/agents/conductors/clone/_clone.py": {"HowToFit", "PyAutoFit", "PyAutoLabs", "PyAutoLens", "autofit_assistant", "autofit_workspace", "autolens_assistant"},
     "PyAutoBrain/agents/conductors/clone/clone.sh": {"HowToFit", "PyAutoFit", "autofit_workspace", "autolens_assistant"},
     "PyAutoBrain/agents/conductors/community/_community.py": {"Jammy2211", "PyAutoLabs"},
-    "PyAutoBrain/agents/conductors/intake/_intake.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace"},
+    "PyAutoBrain/agents/conductors/intake/_intake.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace"},
     "PyAutoBrain/agents/conductors/profiling/_profiling.py": {"PyAutoLabs", "autolens_profiling"},
     "PyAutoBrain/agents/conductors/profiling/profiling.sh": {"autolens_profiling"},
     "PyAutoBrain/agents/conductors/release/nightly.sh": {"PyAutoLabs", "PyAutoLens"},
-    "PyAutoBrain/agents/conductors/release/rehearse.sh": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
-    "PyAutoBrain/agents/conductors/release/validate.sh": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
+    "PyAutoBrain/agents/conductors/release/rehearse.sh": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
+    "PyAutoBrain/agents/conductors/release/validate.sh": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
     "PyAutoBrain/agents/conductors/workspace/_workspace.py": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoLabs", "PyAutoReduce", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
     "PyAutoBrain/agents/faculties/memory/_memory.py": {"autolens_assistant"},
     "PyAutoBrain/agents/faculties/memory/memory.sh": {"autolens_assistant"},
@@ -541,33 +541,33 @@ def write_claude_md_pointers(root, repos):
     "PyAutoBrain/docs/conf.py": {"PyAutoScientist"},
     "PyAutoBrain/bin/check_skill_line_counts.sh": {"admin_jammy", "autolens_profiling"},
     "PyAutoBrain/bin/clean_slate.sh": {"PyAutoLabs"},
-    "PyAutoBrain/bin/ensure_workspace_labels.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "Jammy2211", "PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "PyAutoCTI", "autocti_workspace", "autocti_workspace_test", "autofit_workspace", "autofit_workspace_test", "autogalaxy_workspace", "autogalaxy_workspace_test", "autolens_workspace", "autolens_workspace_test", "euclid_strong_lens_modeling_pipeline"},
+    "PyAutoBrain/bin/ensure_workspace_labels.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "Jammy2211", "PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "PyAutoCTI", "autocti_workspace", "autocti_workspace_test", "autofit_workspace", "autofit_workspace_test", "autogalaxy_workspace", "autogalaxy_workspace_test", "autolens_workspace", "autolens_workspace_test", "euclid_strong_lens_modeling_pipeline"},
     "PyAutoBrain/bin/install.sh": {"PyAutoFit", "PyAutoLabs", "admin_jammy", "autolens_profiling"},
     "PyAutoBrain/bin/overnight_status.sh": {"PyAutoLabs", "autolens_assistant"},
     "PyAutoBrain/bin/pull_all_main.sh": {"PyAutoLabs"},
-    "PyAutoBrain/bin/version_drift.sh": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
-    "PyAutoBrain/bin/worktree.sh": {"PyAutoArray", "PyAutoCTI", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "admin_jammy", "autolens_workspace"},
-    "PyAutoBrain/tests/test_activity_gate.py": {"HowToFit", "HowToLens", "PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoLens", "autolens_workspace"},
+    "PyAutoBrain/bin/version_drift.sh": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
+    "PyAutoBrain/bin/worktree.sh": {"PyAutoArray", "PyAutoCTI", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "admin_jammy", "autolens_workspace"},
+    "PyAutoBrain/tests/test_activity_gate.py": {"HowToFit", "HowToLens", "PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoLens", "autolens_workspace"},
     "PyAutoBrain/tests/test_clone_conductor.py": {"autofit_assistant", "autolens_assistant"},
     "PyAutoBrain/tests/test_community_conductor.py": {"Jammy2211", "PyAutoFit", "PyAutoLabs", "PyAutoLens", "admin_jammy"},
     "PyAutoBrain/tests/test_mind_commit_guard.py": {"/home/jammy", "PyAutoFit", "PyAutoLabs"},
     "PyAutoBrain/tests/test_policy_seams.py": {"PyAutoFit", "PyAutoLens", "autolens_workspace"},
     "PyAutoBrain/tests/test_review_inplace.py": {"PyAutoArray", "PyAutoLabs"},
     "PyAutoBrain/tests/test_skill_install.py": {"PyAutoLabs"},
     "PyAutoBrain/tests/test_workspace_conductor.py": {"HowToGalaxy", "HowToLens", "autolens_workspace"},
-    "PyAutoHands/autobuild/aggregate_results.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
-    "PyAutoHands/autobuild/build_util.py": {"PyAutoConf"},
+    "PyAutoHands/autobuild/aggregate_results.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
+    "PyAutoHands/autobuild/build_util.py": {"PyAutoNerves"},
     "PyAutoHands/autobuild/bump_colab_urls.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoLabs", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
     "PyAutoHands/autobuild/clone_seed.py": {"autofit_assistant"},
     "PyAutoHands/autobuild/create_analysis_issue.py": {"PyAutoLabs"},
     "PyAutoHands/autobuild/generate_autofit.py": {"autofit_workspace"},
     "PyAutoHands/autobuild/generate_markdown.py": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens"},
-    "PyAutoHands/autobuild/generate_release_notes.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "PyAutoScientist"},
-    "PyAutoHands/autobuild/navigator.py": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoCTI", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens"},
+    "PyAutoHands/autobuild/generate_release_notes.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "PyAutoScientist"},
+    "PyAutoHands/autobuild/navigator.py": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoCTI", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens"},
     "PyAutoHands/autobuild/repro_command.py": {"PyAutoLabs", "autogalaxy_workspace_test"},
     "PyAutoHands/autobuild/run_all.py": {"HowToLens", "PyAutoLabs", "autolens_workspace", "euclid_strong_lens_modeling_pipeline"},
     "PyAutoHands/autobuild/slack_release_notes.py": {"PyAutoArray", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
-    "PyAutoHands/autobuild/tag_and_merge.sh": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens"},
+    "PyAutoHands/autobuild/tag_and_merge.sh": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens"},
     "PyAutoHands/pre_build.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "admin_jammy", "autofit_workspace", "autofit_workspace_developer", "autofit_workspace_test", "autogalaxy_workspace", "autogalaxy_workspace_test", "autolens_assistant", "autolens_workspace", "autolens_workspace_developer", "autolens_workspace_test", "euclid_strong_lens_modeling_pipeline"},
     "PyAutoHands/tests/test_bump_colab_urls.py": {"Jammy2211", "PyAutoFit", "PyAutoLabs", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
     "PyAutoHands/tests/test_generate_markdown.py": {"PyAutoArray", "autolens_workspace"},
@@ -582,11 +582,11 @@ def write_claude_md_pointers(root, repos):
     "PyAutoHeart/heart/checks/profiling_drift.py": {"PyAutoLabs", "autolens_profiling", "autolens_workspace_test"},
     "PyAutoHeart/heart/checks/script_timing.py": {"PyAutoLabs"},
     "PyAutoHeart/heart/checks/test_run.py": {"PyAutoLabs"},
-    "PyAutoHeart/heart/checks/unit_test_timing.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
-    "PyAutoHeart/heart/checks/url_check.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "Jammy2211", "PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
+    "PyAutoHeart/heart/checks/unit_test_timing.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens"},
+    "PyAutoHeart/heart/checks/url_check.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "Jammy2211", "PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLabs", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
     "PyAutoHeart/heart/checks/url_check_live.py": {"PyAutoLabs", "PyAutoLens", "admin_jammy"},
-    "PyAutoHeart/heart/checks/url_sweep.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace", "euclid_strong_lens_modeling_pipeline"},
-    "PyAutoHeart/heart/checks/verify_install.sh": {"PyAutoConf", "PyAutoLabs", "PyAutoLens", "autolens_workspace"},
+    "PyAutoHeart/heart/checks/url_sweep.sh": {"HowToFit", "HowToGalaxy", "HowToLens", "PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace", "euclid_strong_lens_modeling_pipeline"},
+    "PyAutoHeart/heart/checks/verify_install.sh": {"PyAutoNerves", "PyAutoLabs", "PyAutoLens", "autolens_workspace"},
     "PyAutoHeart/heart/checks/version_skew.py": {"PyAutoLabs"},
     "PyAutoHeart/heart/checks/workspace_testmode_timing.py": {"PyAutoLabs", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
     "PyAutoHeart/heart/checks/worktree_drift.sh": {"PyAutoLabs"},
@@ -596,21 +596,21 @@ def write_claude_md_pointers(root, repos):
     "PyAutoHeart/heart/shell/heart_prompt.sh": {"PyAutoLabs"},
     "PyAutoHeart/heart/state.py": {"PyAutoFit"},
     "PyAutoHeart/heart/tick.sh": {"autolens_profiling"},
-    "PyAutoHeart/heart/validate.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace", "autolens_workspace_test"},
+    "PyAutoHeart/heart/validate.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace", "autolens_workspace_test"},
     "PyAutoHeart/scripts/health_audit.sh": {"PyAutoLabs"},
     "PyAutoHeart/scripts/health_release.sh": {"PyAutoLabs"},
     "PyAutoHeart/scripts/health_sync.sh": {"PyAutoLabs", "admin_jammy"},
     "PyAutoHeart/tests/test_ci_status.py": {"PyAutoFit", "PyAutoLens", "autolens_workspace"},
-    "PyAutoHeart/tests/test_dashboard.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace"},
-    "PyAutoHeart/tests/test_manifest_drift.py": {"PyAutoConf", "PyAutoFit", "PyAutoLabs"},
+    "PyAutoHeart/tests/test_dashboard.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace"},
+    "PyAutoHeart/tests/test_manifest_drift.py": {"PyAutoNerves", "PyAutoFit", "PyAutoLabs"},
     "PyAutoHeart/tests/test_noise.py": {"HowToFit", "autolens_workspace_test"},
-    "PyAutoHeart/tests/test_readiness.py": {"HowToLens", "PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autogalaxy_workspace", "autolens_workspace", "autolens_workspace_test"},
+    "PyAutoHeart/tests/test_readiness.py": {"HowToLens", "PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autogalaxy_workspace", "autolens_workspace", "autolens_workspace_test"},
     "PyAutoHeart/tests/test_repo_config.py": {"PyAutoCTI", "autocti_workspace", "autocti_workspace_test"},
     "PyAutoHeart/tests/test_state.py": {"PyAutoArray", "PyAutoFit"},
     "PyAutoHeart/tests/test_test_run.py": {"autofit_workspace", "autolens_workspace"},
     "PyAutoHeart/tests/test_unit_test_timing.py": {"PyAutoFit"},
     "PyAutoHeart/tests/test_url_check.py": {"HowToFit", "HowToGalaxy", "HowToLens", "Jammy2211", "PyAutoFit", "PyAutoLabs", "autofit_workspace", "autogalaxy_workspace", "autolens_workspace"},
-    "PyAutoHeart/tests/test_validate.py": {"PyAutoArray", "PyAutoConf", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace", "autolens_workspace_test"},
+    "PyAutoHeart/tests/test_validate.py": {"PyAutoArray", "PyAutoNerves", "PyAutoFit", "PyAutoGalaxy", "PyAutoLens", "autolens_workspace", "autolens_workspace_test"},
     "PyAutoHeart/tests/test_verify_install_script.py": {"Jammy2211", "PyAutoLabs", "autolens_workspace"},
     "PyAutoHeart/tests/test_version_skew.py": {"HowToFit", "PyAutoFit", "PyAutoLens", "autofit_workspace", "autolens_assistant", "autolens_workspace", "autolens_workspace_test"},
     "PyAutoHeart/tests/test_workspace_testmode_timing.py": {"autolens_workspace"},