docs: remove phase labels and organize guides by topic

.github/workflows/scientific-tests.yml

@@ -40,7 +40,7 @@ jobs:
       - name: Install optional official wwPDB XML parser
         run: Rscript -e 'install.packages("xml2", repos="https://cloud.r-project.org")'
         shell: bash
-      - name: Verify Phase C geometry, ensembles and offline CLI
+      - name: Verify geometry, ensembles and offline CLI
         run: |
           Rscript tests/geometry.R
           Rscript tests/experimental.R

.github/workflows/ui-preview.yml

@@ -6,6 +6,7 @@ on:
       - "shinyRam/app.R"
       - "shinyRam/www/**"
       - "tests/ui-browser.cjs"
+      - "tests/structure-verification-browser.cjs"
       - "tests/reports.R"
       - "tests/model-integration.R"
       - "shinyRam/R/**"
@@ -74,7 +75,7 @@ jobs:
       - name: Verify AlphaFold and ESMFold uploads in the live browser
         run: node tests/prediction-browser.cjs
       - name: Verify official wwPDB evidence, density UI and NMR ensemble
-        run: node tests/phase-c-browser.cjs
+        run: node tests/structure-verification-browser.cjs
       - name: Archive desktop/mobile screenshot previews and logs
         if: always()
         uses: actions/upload-artifact@v4

.github/workflows/wwpdb-validation.yml

@@ -8,7 +8,7 @@ on:
       - "benchmarks/wwpdb_helpers.R"
       - "benchmarks/compare_wwpdb.R"
       - "tests/wwpdb.R"
-      - "tests/phase-a-baseline.R"
+      - "tests/wwpdb-baseline.R"
       - "validation/**"
       - ".github/workflows/wwpdb-validation.yml"
   pull_request:
@@ -17,7 +17,7 @@ on:
       - "benchmarks/wwpdb_helpers.R"
       - "benchmarks/compare_wwpdb.R"
       - "tests/wwpdb.R"
-      - "tests/phase-a-baseline.R"
+      - "tests/wwpdb-baseline.R"
       - "validation/**"
       - ".github/workflows/wwpdb-validation.yml"
   workflow_dispatch:
@@ -79,7 +79,7 @@ jobs:
         env:
           ACCESSION: ${{ matrix.accession }}
         run: |
-          Rscript tests/phase-a-baseline.R "$ACCESSION"             "benchmarks/output/wwpdb/$ACCESSION"
+          Rscript tests/wwpdb-baseline.R "$ACCESSION"             "benchmarks/output/wwpdb/$ACCESSION"
       - name: Add independent validation summary
         if: success()
         shell: bash

README.md

@@ -67,13 +67,13 @@ Rscript scripts/ramplotr-batch.R --input structures/ --output results/ --report
 
 The offline command produces per-residue CSV, machine-readable JSON and a batch summary; `--report` additionally requests SVG and standalone HTML reports. For a compatible multi-model structure, add `--ensemble-models 20`. Use `--help` for all options, including declared prediction provenance and an optional matching wwPDB validation XML.
 
-See the [batch-analysis instructions](docs/phase-c-guide.md#offline-batch-mode) for examples and resource limits.
+See the [batch-analysis instructions](docs/structural-verification.md#offline-batch-mode) for examples and resource limits.
 
 ## Scientific interpretation
 
 RamplotR's **residue-aware mode** evaluates general residues, glycine, proline and pre-proline against their corresponding bundled reference distributions. The selected plotting background is independent of those residue-specific classification calculations. The original density references trace back to the distributions discussed by [Lovell et al. (2003)](https://pubmed.ncbi.nlm.nih.gov/12557186/); other bundled reference datasets can also be selected.
 
-**RamplotR region labels are not interchangeable with MolProbity or wwPDB classifications.** They use different reference populations, residue treatments and region definitions. Our [independent validation results](docs/phase-a-results.md), [reproducible protocol](docs/wwpdb-validation.md) and [pinned experimental-structure corpus](validation/manifest.csv) document agreement in calculated angles as well as differences in classification. For deposited experimental structures, attach the official report for the **same structure and model** when making independent quality assessments.
+**RamplotR region labels are not interchangeable with MolProbity or wwPDB classifications.** They use different reference populations, residue treatments and region definitions. Our [independent validation results](docs/validation-results.md), [reproducible protocol](docs/wwpdb-validation.md) and [pinned experimental-structure corpus](validation/manifest.csv) document agreement in calculated angles as well as differences in classification. For deposited experimental structures, attach the official report for the **same structure and model** when making independent quality assessments.
 
 For predictions, pLDDT and PAE describe model confidence rather than experimental verification. ESMFold normally provides pLDDT but not PAE; experimental thermal B-factors are **never** automatically interpreted as prediction confidence. The native ω, χ1 and Cβ measurements are descriptive, and visualising a density map is not a quantitative map–model fit measurement.
 
@@ -82,9 +82,9 @@ The default RamplotR teal contour palette provides consistent, recognisable publ
 ## Documentation
 
 - [Interactive inspection, colours, comparisons and exports](docs/inspection-user-guide.md)
-- [AlphaFold, ColabFold and ESMFold confidence analysis](docs/phase-b-guide.md)
-- [Geometry, official wwPDB evidence, cryo-EM overlays, ensembles and batch mode](docs/phase-c-guide.md)
-- [Independent wwPDB validation protocol and benchmark results](docs/wwpdb-validation.md) · [Results](docs/phase-a-results.md)
+- [AlphaFold, ColabFold and ESMFold confidence analysis](docs/prediction-confidence.md)
+- [Geometry, official wwPDB evidence, cryo-EM overlays, ensembles and batch mode](docs/structural-verification.md)
+- [Independent wwPDB validation protocol and benchmark results](docs/wwpdb-validation.md) · [Results](docs/validation-results.md)
 - [Performance and large-structure benchmarks](docs/benchmark-results.md) · [Scaling results](docs/scaling-results.md)
 
 Developers can run the pure-R scientific regression suite from the repository root with `Rscript tests/scientific.R`. Additional tests cover structure parsing, validation imports, confidence formats, geometry, ensembles and the batch CLI. GitHub Actions also exercises the application in a real browser and runs the scientific tests on Ubuntu and Windows.

docs/README.md

@@ -0,0 +1,18 @@
+# RamplotR documentation
+
+Choose a guide by the research task you want to perform. The [main README](../README.md) introduces the application, screenshots and installation.
+
+## Working with structures
+
+- [Interactive inspection and publication-ready figures](inspection-user-guide.md): linked Ramachandran plot, residue table, sequence navigator, 3D viewer, comparison and exports.
+- [AlphaFold, ColabFold and ESMFold confidence](prediction-confidence.md): model imports, pLDDT and linked PAE inspection.
+- [Structural verification, cryo-EM overlays and ensembles](structural-verification.md): measured backbone/side-chain geometry, independent official reports, maps and offline batch processing.
+
+## Scientific validation and performance
+
+- [Independent wwPDB validation method](wwpdb-validation.md) and [five-structure results](validation-results.md).
+- [Benchmark results](benchmark-results.md), [scaling study](scaling-study.md) and [scaling measurements](scaling-results.md).
+
+## Development records
+
+[Implementation and verification history](development/README.md) is kept separately from the user guides. Its historical notes describe what changed during development, not different current application modes.

docs/development/README.md

@@ -0,0 +1,12 @@
+# Development and verification history
+
+These records document the implementation of RamplotR's current capabilities. They are retained for traceability and are **not** separate application versions or user workflows. Start with the [user documentation](../README.md) instead.
+
+- [Scientific corrections, reference handling and performance](scientific-upgrade.md)
+- [Interactive interface and linked residue inspection](interface-and-inspection.md)
+- [Earlier interface design and browser verification](interface-refresh.md)
+- [Independent experimental validation](independent-validation.md)
+- [AlphaFold and ESMFold prediction-confidence integration](prediction-confidence.md)
+- [Extended geometry, wwPDB evidence, ensemble and batch implementation](structural-verification.md)
+
+The [historical release tag](https://github.com/BiKC/RamplotR/tree/v0.1.0-legacy) remains available for reproducing earlier analyses.

docs/phase-a-worklog.md → docs/development/independent-validation.md

@@ -1,4 +1,4 @@
-# Phase A: independent structural validation
+# Independent experimental validation: implementation record
 
 Base: main at a09d3eed4800bbe5c3aea37869fb181ea8fc8a6f. Historical version v0.1.0-legacy and reference grids are unchanged.
 
@@ -8,17 +8,17 @@ Base: main at a09d3eed4800bbe5c3aea37869fb181ea8fc8a6f. Historical version v0.1.
 - [x] Test XML parsing, stable residue matching, alt locations, insertion codes, missing angles and unequal classification vocabularies.
 - [x] Add a public manifest and an easy-to-run verification workflow; fail CI on coverage/angle regressions, not on genuine differences between reference models.
 - [x] Document why the four-region, four-reference-group RamplotR original method is not directly MolProbity-equivalent to its three regions and six groups.
-- [x] Pass Ubuntu/Windows scientific regression, independent five-structure wwPDB validation, structure-validation benchmark and full live-browser CI, and merge PR #13 into main. ESMFold and AlphaFold are explicitly Phase B.
+- [x] Pass Ubuntu/Windows scientific regression, independent five-structure wwPDB validation, structure-validation benchmark and full live-browser CI, and merge PR #13 into main. AlphaFold and ESMFold prediction confidence are documented separately.
 
 ## Independent findings
 
-[Five-structure results](phase-a-results.md) and
-[pinned SHA256 source manifests](../validation/baseline-source-hashes-2026-09-28.csv)
+[Five-structure results](../validation-results.md) and
+[pinned SHA256 source manifests](../../validation/baseline-source-hashes-2026-09-28.csv)
 were generated from official wwPDB validation reports. 2DQ4's seven official
 outliers are not classified as outliers by the original RamplotR references.
 The independent numerical geometry and group-specific class comparisons are
-tested separately. Do not claim MolProbity-equivalent categories. Phase B
-includes AlphaFold and ESMFold predicted-model confidence integration.
+tested separately. Do not claim MolProbity-equivalent categories. Prediction-confidence analysis for AlphaFold and ESMFold is documented
+in the separate [prediction-confidence guide](../prediction-confidence.md).
 
 Completed integration: https://github.com/BiKC/RamplotR/pull/13
 Reviewed independent validation workflow: https://github.com/BiKC/RamplotR/actions/runs/36476627652

docs/upgrade-inspection-worklog.md → docs/development/interface-and-inspection.md

@@ -1,4 +1,4 @@
-# RamplotR inspection and publication upgrade
+# Interactive inspection and publication tools: implementation record
 
 Branch: `upgrade/inspection-visualization-reporting` (integration PR #12).
 Historical reference: `v0.1.0-legacy` is unchanged; all scientific reference grids are preserved.
@@ -22,7 +22,7 @@ Historical reference: `v0.1.0-legacy` is unchanged; all scientific reference gri
 - [Structure validation and benchmark](https://github.com/BiKC/RamplotR/actions/runs/36470803613)
 - [Live Shiny browser test and visual-preview artifact](https://github.com/BiKC/RamplotR/actions/runs/36470803548)
 
-These runs confirm the implemented regression and browser scenarios. Independent agreement of every RamplotR region classification against MolProbity is separate future validation, not a claim from these tests. Hosted deployments must be updated separately from merging the GitHub repository.
+These runs confirm the implemented regression and browser scenarios. Independent wwPDB comparisons have since been performed and are documented in the [validation results](../validation-results.md). These are method comparisons, not a claim of identical RamplotR and MolProbity classifications. Hosted deployments must be updated separately from merging the GitHub repository.
 
 ## Scientific boundaries
 

docs/interface-refresh.md → docs/development/interface-refresh.md

@@ -1,6 +1,6 @@
-# Interface refresh
+# Interactive interface: design and verification record
 
-The interface refresh changes the layout and plotting presentation without
+This historical record describes the layout and plotting changes without
 changing backbone extraction, reference grids or scientific classifications.
 The historical application remains available as v0.1.0-legacy.
 
@@ -71,6 +71,6 @@ In a browser, check both a wide desktop window and a mobile-width window:
 5. Test a structure with many chains and a structure with missing angles,
    then download a PNG with the Plotly toolbar.
 
-The old README screenshot is historical; capture a new screenshot from a
-running app before replacing it. The shinyapps.io deployment is separate
+The [main README](../../README.md) now contains curated screenshots generated
+from the real browser tests. The shinyapps.io deployment is separate
 from merging changes into the GitHub repository.

docs/phase-b-worklog.md → docs/development/prediction-confidence.md

@@ -1,6 +1,6 @@
-# Phase B — AlphaFold and ESMFold confidence integration
+# Prediction confidence: implementation record
 
-Base: main `99fd7f38c17e88dce28b043560ecd5a147d647ea`. Scientific Phase A and historical tag stay unchanged.
+Base: main `99fd7f38c17e88dce28b043560ecd5a147d647ea`. Independent validation and the historical tag remain unchanged.
 
 - [x] Native prediction provenance and per-residue pLDDT extraction from AlphaFold and ESMFold B-factors; experimental B-factors must never be relabelled confidence.
 - [x] Optional AlphaFold DB accession retrieval and JSON confidence sidecar uploads (AlphaFold 2 PAE and AlphaFold 3 full confidence/summary JSON).

docs/upgrade-worklog.md → docs/development/scientific-upgrade.md

@@ -1,14 +1,14 @@
 # RamplotR upgrade worklog
 
-This log records the main changes and their verification status. Work happens in separately scoped commits. The published historical baseline is preserved as `v0.1.0-legacy` (commit `aa3eba2180d505f4dc01c9c2bf977cef00b3252a`).
+This historical log records early scientific changes and verification. For current usage, see [the documentation index](../README.md). Some unchecked historical proposals were subsequently implemented in other pull requests; refer to the current user guides for available features. Work happens in separately scoped commits. The published historical baseline is preserved as `v0.1.0-legacy` (commit `aa3eba2180d505f4dc01c9c2bf977cef00b3252a`).
 
 ## Completed in PR #2
 
 1. Residue-aware classification independent of the plotting background, with an explicit legacy option.
 2. Deterministic density thresholds and reusable reference grids.
 3. Atom-based backbone torsions that respect peptide connectivity, chain boundaries and insertion codes.
 
-## Phase 2: CI, inputs, reproducibility
+## Regression testing, input handling and reproducibility
 
 - [x] Keep scientific changes in their own commits, merged without squashing.
 - [x] Add a two-platform R regression workflow for existing scientific test scripts.
@@ -21,22 +21,22 @@ This log records the main changes and their verification status. Work happens in
 
 The scientific classifications are tied to the bundled reference densities. Do not claim MolProbity-equivalent outlier percentages without a separate benchmark. New methods and reference datasets will be versioned.
 
-## Phase 3: scientific comparisons and timing
+## Scientific comparisons and timing
 
 - [x] Provide a repeatable analysis/timing script recording the structure, reference dataset, software environment and per-stage elapsed time.
 - [x] Provide an independent torsion-angle comparison with Bio3D for PDB accessions without insertion codes.
 - [x] Correct Bio3D whitespace-padded residue identifiers and require at least 98% comparison coverage: 45 phi and 45 psi comparisons for 1CRN; 2,880 of each for 6VXX, with zero differences over 0.5 degrees.
 - [ ] Run scaling benchmarks on large PDB/mmCIF inputs and record benchmark output.
 - [ ] Compare region labels against independently generated structural-validation reports; numerical thresholds differ across implementations.
 
-## Phase 4: larger-structure performance and paper preparation
+## Larger-structure performance and manuscript planning
 
 - [x] Preallocate and vectorize backbone extraction (PR #5).
 - [x] Cache immutable classification reference profiles (PR #6).
 - [x] Correct independent validation identifier matching and enforce coverage (PR #7).
 - [x] Run a same-runner 6VXX scaling pilot with 1x, 3x and 10x replicated
   complexes and record peak RSS, warm/cold stage timings and software metadata.
-  See [measured results](scaling-results.md) and [run 36430181464](https://github.com/BiKC/RamplotR/actions/runs/36430181464).
+  See [measured results](../scaling-results.md) and [run 36430181464](https://github.com/BiKC/RamplotR/actions/runs/36430181464).
 - [ ] Run paired same-host comparisons of legacy and current algorithms, including peak RSS.
 - [ ] Compare RamplotR region labels against independent MolProbity-style reports.
 - [ ] Prepare the methods, validation tables and figures for the arXiv preprint once validation is complete.