Restructure PyAutoMind prompts by work type

[Jammy2211]

Implements autoprompt/redesign.md. Reorganises the prompt repository so the first folder level describes the kind of work, and the second names the target repo/domain — so PyAutoBrain can route intent to the right specialist agent by reading the first path segment.

PyAutoMind organises intent by the kind of thinking required; PyAutoBrain uses that structure to choose the right reasoning agent.

New taxonomy

First folder = work type, second = target. Work types: feature/ bug/ refactor/ docs/ test/ release/ maintenance/ research/ experiment/, plus triage/ for prompts whose classification is still unclear.

Folder	Future PyAutoBrain agent
feature/	feature planner
bug/	debugger
refactor/	refactor architect
docs/	documentation agent
test/	test engineer
release/	release engineer
maintenance/	hygiene agent
research/	research analyst
experiment/	prototype agent

Current active-prompt counts: feature 30, bug 21, research 8, docs 3, test 3, refactor 2, maintenance 2.

What moved

• All 69 active prompts moved into <work-type>/<target>/ via git mv (history preserved). The old repo-named top-level folders (autoarray/, autofit/, autogalaxy/, autolens/, autolens_assistant/, autobrain/ → feature/pyautobrain/, autobuild/, workspaces/, visualization/, …) are gone.
• Numbered topic series (jax_substructure, weak, cluster, priors) kept together under their dominant work type rather than scattered across folders, preserving ordering and their trackers.
• One ambiguous prompt (jax_zero_contour.md) parked in triage/ with a manual-review note.

Examples of moved prompts:

• autoarray/oversampling.md → feature/autoarray/oversampling.md
• autogalaxy/spherical_bug.md → bug/autogalaxy/spherical_bug.md
• autofit/latent_class_redesign.md → refactor/autofit/latent_class_redesign.md
• autoarray/delaunay_research.md → research/autoarray/delaunay_research.md
• autolens_assistant/science_project_collaborator_clone.md → docs/autolens_assistant/...
• priors/* (audit series) → bug/priors/*

Preserved as lifecycle / meta (not work-types)

issued/, z_features/, z_vault/, shelved/ keep their own names; autoprompt/ remains the meta folder for prompts about this repo's own infrastructure.

References updated

• planned.md prompt paths; the z_features trackers (cluster / jax_substructure / weak) and the priors in-folder tracker.
• Repaired some pre-existing rotten links to already-shipped cluster/weak prompts (repointed to issued/).
• scripts/status.sh inventory is now work-type aware; AGENTS.md layout and the start_dev / create_issue / register_and_iterate skill docs updated.
• README: new "Prompt taxonomy" section (work-type → agent map, good prompt paths, optional metadata-header convention, migration note). Added ROUTING.md and triage/README.md.

Compatibility notes

Routing keys off @RepoName references in a prompt's body, not its folder — so the skills accept both old <target>/<name>.md and new <work-type>/<target>/<name>.md paths during the transition. PyAutoBrain agents are not implemented here; only the taxonomy + metadata are defined, per the prompt.

Validation

• bash scripts/status.sh runs clean and lists the new work-type inventory.
• A link-resolution sweep across the z_features trackers and the priors series passes (all relative .md links resolve).
• No live references to removed folders remain outside intentional historical records (issued/, complete.md, queue.md DONE entries).

Follow-up tasks for PyAutoBrain agent routing

• Implement the agents in PyAutoBrain (PyAutoAgent) that consume the first-folder work type per ROUTING.md.
• Re-home triage/jax_zero_contour.md once its work type is confirmed (likely test/autolens_workspace_test/).
• Classifications are subjective; a few (e.g. the whole priors audit under bug/, nufft_simulator_chunking under feature/ vs bug/) are one git mv to adjust if preferred.

🤖 Generated with Claude Code

https://claude.ai/code/session_01MMS6B2CqwaLwBfWGZRtCT9

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Generated by Claude Code

[Copilot]

Pull request overview

This PR restructures PyAutoMind prompts into a new taxonomy where the first path segment indicates work type (feature/bug/refactor/docs/test/release/maintenance/research/experiment), enabling PyAutoBrain to route work based on folder classification. It also updates core documentation, skills, and trackers to reflect the new layout and introduces ROUTING.md + triage/ guidance for uncategorized prompts.

Changes:

• Define and document the work-type → agent routing contract (ROUTING.md) and update repository docs (README.md, AGENTS.md) accordingly.
• Update operational tooling and skills to understand the new path layout (scripts/status.sh, skills/*), plus refresh trackers/registries to point at moved prompts.
• Add new prompts organized under the new taxonomy (including new triage/ holding area and new work-type/target prompt files).

Reviewed changes

Copilot reviewed 14 out of 82 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
z_features/weak_shear.md	Updates weak-lensing epic tracker links to new/issued prompt locations.
z_features/jax_substructure_simulator.md	Updates tracker links to feature/jax_substructure/*.
z_features/cluster_lensing.md	Updates cluster epic tracker links to issued/ and feature/cluster/*.
triage/README.md	Adds documentation for the non-routed triage holding area.
triage/jax_zero_contour.md	Adds a triaged prompt with an HTML comment indicating it needs manual classification.
test/workspaces/smoke_workspace_fixes.md	Adds a test-oriented prompt capturing smoke-test failures and follow-up fixes.
test/workspaces/restore_workspace_test_likelihood_baselines.md	Adds a test-oriented prompt to restore absolute NumPy regression baselines in _workspace_test repos.
test/autolens_workspace_developer/mge_jit_regression_rebaseline.md	Adds a test/developer prompt to re-baseline a profiling regression constant.
skills/start_dev/start_dev.md	Updates /start_dev documentation and parsing rules to accept work-type paths.
skills/register_and_iterate/register_and_iterate.md	Updates queue/registry prompt-path documentation for work-type layout.
skills/create_issue/SKILL.md	Updates /create-issue usage examples for work-type paths.
scripts/status.sh	Makes inventory reporting work-type aware (plus separate lifecycle/meta section).
ROUTING.md	New routing contract documenting work-type → PyAutoBrain agent mapping.
research/autolens_workspace_developer/jax_jit_profiling.md	Adds a research prompt about profiling JIT compilation latency.
research/autobuild/git_docs.md	Adds a research prompt about GitHub/ReadTheDocs documentation strategy.
refactor/autogalaxy/einstein_radius_jit_native_seed_finder.md	Adds a refactor prompt describing a JAX-native seed-finder approach.
README.md	Updates repo layout + adds “Prompt taxonomy” documentation and migration note.
planned.md	Updates planned registry entries to new prompt paths.
maintenance/workspaces/read_through_issues.md	Adds a maintenance prompt with workspace cleanup/tasks list.
maintenance/autolens_profiling/polish.md	Adds a maintenance prompt for consolidating and validating profiling workflows/results.
feature/workspaces/restore_multiple_sources_lensing_of_lens.md	Adds a workspace feature prompt gated on an external PyAutoLens issue.
feature/workspaces/group_subhalo_sensitivity.md	Adds a workspace feature prompt for group subhalo sensitivity mapping.
feature/workspaces/group_los_halos.md	Adds a workspace feature prompt for group LOS-halo examples.
feature/weak/5_likelihood_function.md	Adds a feature prompt to write weak-lensing likelihood tutorial script.
feature/weak/4_modeling.md	Adds a feature prompt to implement weak-lensing modeling modules mirroring imaging API.
feature/pyautobrain/health.md	Adds a feature prompt to implement a PyAutoBrain Health Agent.
feature/pyautobrain/feature.md	Adds a feature prompt describing a PyAutoBrain Feature Agent design/behavior.
feature/pyautobrain/build.md	Adds a feature prompt describing a PyAutoBrain Build Agent design/behavior.
feature/jax_substructure/6_deflection_equivalence_test.md	Adds a feature prompt for a new deflection-equivalence integration test.
feature/jax_substructure/5_prng_key_vmap_noise.md	Adds a feature prompt to thread PRNG keys through Poisson-noise APIs for vmap.
feature/jax_substructure/4_vmap_batched_simulation.md	Adds a feature prompt for vmapped batched simulation and memory considerations.
feature/jax_substructure/3_simulator_jax_e2e.md	Adds a feature prompt wiring scan/vmap ray-tracing through PSF+noise for E2E JIT simulate.
feature/jax_substructure/2_tracer_lax_scan.md	Adds a feature prompt replacing nested loops with jax.lax.scan for multi-plane tracing.
feature/jax_substructure/1_vmap_subhalo_deflections.md	Adds a feature prompt for vmapped per-plane deflection computation and tests.
feature/cluster/5_profiling.md	Adds a feature prompt to add cluster likelihood profiling scripts.
feature/autolens_assistant/script_to_notebook.md	Adds a feature prompt for narrative-docstring script → notebook conversion tooling.
feature/autolens_assistant/science_project_per_project_literature.md	Adds a feature prompt defining project-local vs shared literature handling.
feature/autolens_assistant/science_project_assistant_ref.md	Adds a feature prompt for assistant resolution/provenance pinning in science projects.
feature/autolens_assistant/science_project_api_gate.md	Adds a feature prompt for reusing the assistant’s API validation gate in projects.
feature/autolens_assistant/portable_user_defaults.md	Adds a feature prompt about environment discovery and optional portable defaults.
feature/autolens_assistant/live_visual_update_context.md	Adds a feature prompt to surface live visualization options in assistant guidance.
feature/autogalaxy/point_source_light.md	Adds a feature prompt proposing a point-source light profile and constraints.
feature/autogalaxy/piemass_potential.md	Adds a feature prompt to implement missing PIEMass lensing potential.
feature/autofit/ep_lbfgs_jax.md	Adds a feature prompt about scaling EP framework / alternative optimizers.
feature/autoarray/rectangular_multi_submesh.md	Adds a feature prompt for multi-sub-mesh rectangular adaptation (Path B).
feature/autoarray/rectangular_adapt_constant_split_guard.md	Adds a feature prompt to guard invalid mesh+regularization combinations.
feature/autoarray/oversampling.md	Adds a feature prompt to implement oversampled PSF convolution support.
feature/autoarray/nufft_simulator_chunking.md	Adds a feature prompt to add chunking to NUFFT simulator path to avoid OOMs.
feature/autoarray/multiwavelength_inversion.md	Adds an (incomplete/draft) feature prompt for multiwavelength inversion approach.
feature/autoarray/arcsecond_to_decimal.md	Adds a feature prompt to change arcsecond tick label formatting via plotting API.
docs/workspaces/preloads_advanced_workspace_guide.md	Adds a docs prompt for an advanced Preloads guide in workspaces.
docs/workspaces/add_vincken_2026_wiki_and_cite_in_euclid.md	Adds a docs prompt to ingest/cite a paper in downstream paper repos.
docs/autolens_assistant/science_project_collaborator_clone.md	Adds a docs prompt to clarify collaborator cloning + assistant refer-back model.
bug/priors/z_features.md	Updates priors/messages audit tracker references for new repo/taxonomy.
bug/priors/13_collapse_prior_and_message.md	Adds a bug-tracker prompt for a large refactor/design discussion.
bug/priors/12_single_source_density_refactor.md	Adds a bug-tracker prompt for density single-source-of-truth refactor design.
bug/priors/11_transformed_message_semantics_doc.md	Adds a bug-tracker prompt documenting transform semantics and potential rename.
bug/priors/10_fixed_message_cache_growth.md	Adds a bug-tracker prompt about unbounded cache growth in FixedMessage.
bug/priors/09_prior_property_tests.md	Adds a bug-tracker prompt proposing property-based tests for priors/messages.
bug/priors/08_relative_width_modifier_safety.md	Adds a bug-tracker prompt about sigma sign/zero safety in width modifiers.
bug/priors/07_log_prior_normalisation_convention.md	Adds a bug-tracker prompt about inconsistent log-prior normalization conventions.
bug/priors/06_normal_message_sigma_negative_unchecked.md	Adds a bug-tracker prompt about NormalMessage sigma validation and JAX behavior.
bug/priors/05_inv_beta_suffstats_clamp_noop.md	Adds a bug-tracker prompt about a clamp no-op in beta sufficient-stat inversion.
bug/priors/04_truncated_normal_log_partition_incomplete.md	Adds a bug-tracker prompt about truncated normal log-partition missing Gaussian term.
bug/priors/03_gamma_from_mode_wrong_formula.md	Adds a bug-tracker prompt about incorrect GammaMessage.from_mode formula.
bug/priors/02_uniform_logpdf_array_handling.md	Adds a bug-tracker prompt about UniformPrior.logpdf scalar-only boundary handling.
bug/priors/01_log_gaussian_with_limits_crash.md	Adds a bug-tracker prompt about LogGaussianPrior.with_limits crash.
bug/autolens/pixelization_eager_vs_jit_divergence.md	Adds a bug prompt investigating eager vs JIT divergence in pixelization likelihoods.
bug/autogalaxy/spherical_bug.md	Adds a bug prompt flagging a likely spherical/geometry naming issue.
bug/autogalaxy/nfw_truncated_potential_accuracy.md	Adds a bug prompt about NFWTruncated potential self-consistency failure.
bug/autofit/messages_xp_stack_jax_trace.md	Adds a bug prompt about JAX tracing failures from xp.array([...]) patterns.
bug/autofit/factor_graph_3_14_instance_iteration.md	Adds a bug prompt about FactorGraphModel instance shape regression on Python 3.14.
bug/autoarray/rect_adapt.md	Adds a bug prompt about potential plotting alignment issues for rectangular meshes.
AGENTS.md	Updates AI-agent guidance to the new prompt taxonomy and lifecycle/meta folders.

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