Use declarative category identity metadata (#177)

* Document verbosity category and workspace.cif layout

* Reorganize development documentation structure

* Tighten workspace migration plan for autonomous implementation

* Consolidate ADR index into single table

* Add loop category key identity ADR and plan

* Add declarative category identity resolution

* Declare category identities on current items

* Persist explicit constraint identifiers

* Update ADR for declarative category identity

* Verify declarative category identity behavior

Author: AndrewSazonov

.github/copilot-instructions.md

@@ -34,7 +34,10 @@
 - One class per file when substantial; group small related classes.
 - No `**kwargs` — use explicit keyword arguments.
 - No string-based dispatch (e.g. `getattr(self, f'_{name}')`); write
-  named methods (`_set_sample_form`, `_set_beam_mode`).
+  named methods (`_set_sample_form`, `_set_beam_mode`). Narrow framework
+  metadata lookups are allowed when the attribute name is a class-level
+  declaration, is not user input, and is validated in one central place;
+  for example, `CategoryItem._category_entry_name`.
 - Public attrs are either editable (getter+setter property) or read-only
   (getter only). For internal mutation of read-only props, use a private
   `_set_<name>` method, not a public setter.
@@ -77,7 +80,7 @@
 ## Testing
 
 - Every new module, class, or bug fix ships with tests. See
-  `docs/dev/architecture.md` §10 for the full strategy.
+  `docs/dev/adrs/accepted/test-strategy.md` for the full strategy.
 - Unit tests mirror the source tree:
   `src/easydiffraction/<pkg>/<mod>.py` →
   `tests/unit/easydiffraction/<pkg>/test_<mod>.py`. Verify with
@@ -102,8 +105,11 @@
 
 - Before any structural/design change (new categories, factories,
   switchable-category wiring, datablocks, CIF serialisation), read
-  `docs/dev/architecture.md` and follow documented patterns. Localised
-  bug fixes or test updates need only this file.
+  `docs/dev/adrs/index.md` and the relevant accepted ADRs. Localised bug
+  fixes or test updates need only this file.
+- Development documentation lives under `docs/dev/`. Use
+  `docs/dev/adrs/index.md` as the architecture and decision navigation
+  surface; there is no separate `architecture.md` source of truth.
 - Project is in beta: no legacy shims, no deprecation warnings — update
   tests and tutorials to the current API.
 - Minimal diffs; don't reformat working code. Fix only what's asked;
@@ -112,7 +118,10 @@
   resolves them.
 - Never remove or replace existing functionality without explicit
   confirmation — highlight every removal and wait for approval.
-- When renaming, grep the entire project (code, tests, tutorials, docs).
+- When renaming or auditing usages, search the entire project (code,
+  tests, tutorials, docs). Use `git grep -n` because all contributors
+  have Git; do not assume `rg` is installed. If `git grep` is
+  unavailable, fall back to `find ... -type f` plus `grep -n`.
 - Each change is atomic and single-commit-sized: make one change,
   suggest the commit message, then stop and wait for confirmation.
 - When in doubt, ask.
@@ -137,34 +146,45 @@
 
 Non-trivial changes use a two-phase workflow:
 
-- **Phase 1 — Implementation.** Code, docs, and architecture updates
-  only. Do not create or run tests unless the user explicitly asks. When
-  done, present for review and iterate until approved.
+- **Phase 1 — Implementation.** Code and docs updates only. Update ADRs
+  when the change affects architecture or documented decisions. Do not
+  create or run tests unless the user explicitly asks. When done,
+  present for review and iterate until approved.
 - **Phase 2 — Verification.** Add/update tests, then run `pixi run fix`,
   `pixi run check`, `pixi run unit-tests`, `pixi run integration-tests`,
   `pixi run script-tests`.
 
 Notes:
 
-- `pixi run fix` regenerates `docs/dev/package-structure-*.md`
-  automatically — never edit those by hand. Don't review auto-fixes;
-  accept and move on. Then `pixi run check` until clean.
+- `pixi run fix` regenerates `docs/dev/package-structure/full.md` and
+  `docs/dev/package-structure/short.md` automatically — never edit those
+  by hand. Don't review auto-fixes; accept and move on. Then
+  `pixi run check` until clean.
 - Open issues / design questions / planned improvements live in
-  `docs/dev/issues_open.md` (priority-ordered). On resolution, move to
-  `docs/dev/issues_closed.md` and update `architecture.md` if affected.
+  `docs/dev/issues/open.md` (priority-ordered). On resolution, move to
+  `docs/dev/issues/closed.md` and update the relevant ADR or
+  `docs/dev/adrs/index.md` if affected.
 
 ### Planning
 
 When asked to create a plan:
 
+- Start the plan by referencing this file:
+  `.github/copilot-instructions.md`. State any deliberate exception to
+  these instructions in the plan itself.
 - First gather enough repository context to make the plan concrete. Ask
   all ambiguous or unclear questions in one concise batch; record
   unresolved questions in the plan if the user wants it saved before
   answering them.
-- Save plans as `docs/dev/plan_<feature-name>.md` (lowercase,
-  dash-separated, e.g. `plan_background-refactor.md`). Use the same
-  `<feature-name>` for the implementation branch
-  (`feature/<feature-name>`). Do not push the branch unless asked.
+- Save plans as `docs/dev/plans/<feature-name>.md` (lowercase,
+  dash-separated, e.g. `docs/dev/plans/background-refactor.md`). When a
+  plan implements one ADR, use the same slug as the ADR file; for
+  example, `docs/dev/adrs/suggestions/foo.md` maps to
+  `docs/dev/plans/foo.md`. If a plan has no corresponding ADR or spans
+  multiple ADRs, choose a concise feature slug and list all related ADRs
+  in the plan. Use the same `<feature-name>` for the implementation
+  branch (`feature/<feature-name>`). Do not push the branch unless
+  asked.
 - Include a status checklist with `[ ]` items; mark `[x]` as completed
   during implementation.
 - Apply the two-phase workflow (Phase 1 implementation, Phase 2
@@ -184,6 +204,9 @@ When asked to create a plan:
   files likely to change, decisions already made, open questions,
   verification commands for Phase 2, and a short suggested commit
   message or branch name when useful.
+- Before saving a plan, verify that referenced files, directories,
+  scripts, and task names exist locally when that is practical. If a
+  referenced tool is optional or missing, include an available fallback.
 - End every plan with a "Suggested Pull Request" section containing a
   short PR title and a brief end-user-oriented description. Keep this
   section non-technical enough for scientists and other users to

…/dev/ADRs/adr_category-owner-sections.md …adrs/accepted/category-owner-sections.mddocs/dev/ADRs/adr_category-owner-sections.md renamed to docs/dev/adrs/accepted/category-owner-sections.md docs/dev/ADRs/adr_category-owner-sections.md renamed to docs/dev/adrs/accepted/category-owner-sections.md

@@ -0,0 +1,44 @@
+# ADR: Two-Level Category Parameter Access
+
+## Status
+
+Accepted.
+
+## Date
+
+2026-05-17
+
+## Group
+
+Core model.
+
+## Context
+
+EasyDiffraction models CIF concepts as datablocks, categories, category
+collections, and parameters. Users need predictable navigation paths
+from a structure or experiment to any parameter.
+
+## Decision
+
+Use at most two navigation levels from a datablock to a parameter:
+
+```python
+structure.cell.length_a = 3.88
+experiment.instrument.setup_wavelength = 1.494
+structure.atom_sites['Si'].adp_iso = 0.47
+experiment.background['10'].y = 170
+```
+
+The general forms are:
+
+- `DATABLOCK.CATEGORY_ITEM.PARAMETER`
+- `DATABLOCK.CATEGORY_COLLECTION[ITEM_ID].PARAMETER`
+
+Categories are flat siblings under their owner. A category must not own
+another category of a different type.
+
+## Consequences
+
+API paths remain short, regular, and close to CIF category structure.
+Nested category designs are rejected because they make parameter access
+depth depend on the domain area and obscure the CIF-like model.

docs/dev/adrs/accepted/category-parameter-access.md

@@ -0,0 +1,66 @@
+# ADR: Development Documentation Structure
+
+## Status
+
+Accepted.
+
+## Date
+
+2026-05-17
+
+## Group
+
+Documentation.
+
+## Context
+
+Development notes, ADRs, roadmap material, package-structure snapshots,
+and issue backlogs were all kept directly under `docs/dev` or under
+mixed-case directories. That made the development documentation harder
+to scan and created several competing naming conventions.
+
+The repository also contains `docs/docs`, which is the MkDocs source for
+published user documentation. Development-only material should not be
+mixed into that tree unless it is intentionally published.
+
+## Decision
+
+Keep development-only documentation under `docs/dev`.
+
+Use this structure:
+
+```text
+docs/dev/
+|-- index.md
+|-- adrs/
+|   |-- index.md
+|   |-- accepted/
+|   `-- suggestions/
+|-- issues/
+|   |-- open.md
+|   `-- closed.md
+|-- package-structure/
+|   |-- full.md
+|   `-- short.md
+|-- plans/
+`-- roadmap/
+    `-- ROADMAP.md
+```
+
+Use lowercase directory names for new development-doc folders. Keep
+`ROADMAP.md` uppercase because it may later be copied into published
+user documentation where the conventional filename is useful.
+
+Use `docs/dev/adrs/index.md` as the architecture and decision navigation
+surface. Do not keep a separate architecture overview that duplicates
+ADR content.
+
+## Consequences
+
+- Development documentation remains under the documentation tree without
+  being part of the published MkDocs source by default.
+- ADRs have one entry point for architecture navigation and separate
+  accepted and proposed areas.
+- Package-structure snapshots have stable, script-friendly paths.
+- Roadmap publication can later be implemented as a build-time copy from
+  `docs/dev/roadmap/ROADMAP.md` into `docs/docs`.

docs/dev/adrs/accepted/development-docs-structure.md

@@ -0,0 +1,34 @@
+# ADR: Enum-Backed Closed Value Sets
+
+## Status
+
+Accepted.
+
+## Date
+
+2026-05-17
+
+## Group
+
+Core model.
+
+## Context
+
+Many attributes accept a finite set of values: experiment axes, factory
+tags, fit modes, calculators, minimizers, and rendering engines.
+String-only dispatch is hard to grep and easy to mistype.
+
+## Decision
+
+Represent every finite closed set with a `(str, Enum)` class.
+
+Use enum members as the internal source of truth for validation,
+dispatch, default rules, and descriptions. User-facing setters may
+accept either enum members or their string values, but internal code
+compares against enum members.
+
+## Consequences
+
+Finite choices are discoverable, type-checkable, and greppable.
+Validation can use enum membership instead of hand-written string
+patterns.

docs/dev/ADRs/adr_display-ux.md docs/dev/adrs/accepted/display-ux.mddocs/dev/ADRs/adr_display-ux.md renamed to docs/dev/adrs/accepted/display-ux.md

@@ -0,0 +1,44 @@
+# ADR: Factory Contracts and Metadata
+
+## Status
+
+Accepted.
+
+## Date
+
+2026-05-17
+
+## Group
+
+Factories.
+
+## Context
+
+Many domain categories have multiple implementations, and some currently
+have only one implementation but may gain more later. Construction,
+default selection, compatibility filtering, and supported-option display
+need a common contract.
+
+## Decision
+
+Every category that can be constructed by framework code is created
+through a factory, even when it currently has only one implementation.
+
+Concrete factory-created classes carry metadata appropriate to their
+role:
+
+- `type_info` for stable tag lookup and user descriptions.
+- `compatibility` for experiment-axis compatibility where relevant.
+- `calculator_support` for calculation-engine support where relevant.
+
+Child rows that only exist inside a collection do not carry factory
+metadata; the collection carries the metadata.
+
+Factory registration is triggered by explicit imports in package
+`__init__.py` files.
+
+## Consequences
+
+Construction, default resolution, support tables, and compatibility
+filtering stay uniform. Single-implementation categories are ready for
+future alternatives without changing the public construction pattern.

docs/dev/adrs/accepted/enum-backed-closed-values.md

@@ -0,0 +1,48 @@
+# ADR: Factory Tag Naming
+
+## Status
+
+Accepted.
+
+## Date
+
+2026-05-17
+
+## Group
+
+Naming.
+
+## Context
+
+Factory tags are persisted and used for public selection. Inconsistent
+abbreviations or ordering would make saved files and user code harder to
+read.
+
+## Decision
+
+Canonical factory tags are:
+
+- lowercase
+- hyphen-separated
+- semantically ordered from general to specific
+- unique within a factory
+
+Use standard abbreviations:
+
+| Concept             | Abbreviation |
+| ------------------- | ------------ |
+| Powder              | `pd`         |
+| Single crystal      | `sc`         |
+| Constant wavelength | `cwl`        |
+| Time-of-flight      | `tof`        |
+| Bragg scattering    | `bragg`      |
+| Total scattering    | `total`      |
+
+Context-local aliases are allowed when the owning object already
+disambiguates the choice, for example `pseudo-voigt` inside a CWL
+experiment.
+
+## Consequences
+
+Saved tags are stable and greppable, while user-facing APIs can remain
+short where context makes the canonical prefix redundant.

docs/dev/adrs/accepted/factory-contracts.md

@@ -0,0 +1,39 @@
+# ADR: Free-Flag CIF Encoding
+
+## Status
+
+Accepted.
+
+## Date
+
+2026-05-17
+
+## Group
+
+Persistence.
+
+## Context
+
+Fitting needs to persist whether a parameter is fixed or free. A
+separate free-parameter list would duplicate state already attached to
+individual parameter values and could become stale.
+
+## Decision
+
+Encode a parameter's free/fixed status in the CIF value uncertainty
+syntax:
+
+```text
+3.89     fixed
+3.89(2)  free with estimated standard deviation
+3.89()   free without estimated standard deviation
+```
+
+Do not persist a separate list of free parameters as the source of
+truth.
+
+## Consequences
+
+Each parameter carries its own fit-state information in the same place
+as the value. CIF round-trips are simpler because there is no separate
+state table to reconcile.