Update CLAUDE.md to reflect v1.0.0 release state

- Change status from "v2 implementation complete" to "v1.0.0 released"
- Add documentation section with vignette list and pkgdown URL
- Update diagnostics slot to include residuals, std_residuals, fitted
- Add diagnostics.R and test-diagnostics.R to file structure
- Remove references to deleted spec files
- Simplify development guidelines
- Update terminology from PRM to phosphoproteomics

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: danmaclean

CLAUDE.md

@@ -1,22 +1,22 @@
 # pepdiff
 
-Differential abundance analysis for PRM proteomics data.
+Differential abundance analysis for phosphoproteomics data.
 
 ## Purpose
 
 Identify peptides with significant abundance changes between experimental conditions. Answers: "What's differentially abundant?"
 
 ## Project Status
 
-**v2 implementation complete** (Feb 2026). The package includes:
+**v1.0.0 released** (Feb 2026). The package is feature-complete with:
 - S3 classes: `pepdiff_data` and `pepdiff_results`
 - Three analysis methods: GLM (Gamma + emmeans), ART, pairwise
 - Four pairwise tests: wilcoxon, bootstrap_t, bayes_t, rankprod
+- GLM fit diagnostics with `plot_fit_diagnostics()`
 - Plot methods for both classes
-- 257 passing tests, `devtools::check()` passes with 0 errors/warnings
-- Legacy functions preserved with deprecation warnings
-
-**Next:** Vignettes (see `vignette_plan.md` and `vignette_prompt.md`)
+- Six vignettes covering all workflows
+- pkgdown documentation site: https://teammaclean.github.io/pepdiff/
+- `devtools::check()` passes with 0 errors/warnings
 
 **Companion to peppwR:**
 - peppwR: "How many samples do I need?" (power analysis, planning)
@@ -28,6 +28,17 @@ Identify peptides with significant abundance changes between experimental condit
 CSV → read_pepdiff() → pepdiff_data → compare() → pepdiff_results → plots
 ```
 
+## Documentation
+
+- **Getting Started**: `vignettes/basic_workflow.Rmd`
+- **GLM Analysis**: `vignettes/glm_analysis.Rmd`
+- **ART Analysis**: `vignettes/art_analysis.Rmd`
+- **Pairwise Tests**: `vignettes/pairwise_tests.Rmd`
+- **Checking Model Fit**: `vignettes/checking_fit.Rmd`
+- **Diagnostic Plots**: `vignettes/diagnostic_plots.Rmd`
+
+Online: https://teammaclean.github.io/pepdiff/
+
 ## Design Constraints
 
 ### Cross-Sectional Factorial Designs Only
@@ -72,7 +83,7 @@ Analysis results from `compare()`. Results in **long format** (tidy).
 - `results` - tibble (long): peptide, gene_id, comparison, [factor levels], fold_change, log2_fc, test, p_value, fdr, significant
 - `comparisons` - tibble: comparison definitions
 - `method` - "glm", "art", or "pairwise"
-- `diagnostics` - tibble (nested): peptide, converged, deviance, model, residuals
+- `diagnostics` - tibble (nested): peptide, converged, deviance, residuals, std_residuals, fitted
 - `params` - list: alpha, fdr_method, formula, etc.
 - `data` - the pepdiff_data object used
 - `call` - original function call
@@ -102,7 +113,7 @@ Three methods:
 |--------|-------|----------|
 | `"glm"` (default) | Gamma GLM + emmeans | Most proteomics data |
 | `"art"` | Aligned Rank Transform | Non-parametric alternative |
-| `"pairwise"` | Direct two-group tests | Legacy mode |
+| `"pairwise"` | Direct two-group tests | Simple comparisons |
 
 **Simple interface:**
 ```r
@@ -126,6 +137,13 @@ compare(data,
 - `"bayes_t"` - Bayes factor t-test
 - `"rankprod"` - Rank products
 
+### Diagnostics
+
+```r
+plot_fit_diagnostics(results)
+# Returns 4-panel diagnostic plot for GLM model fit assessment
+```
+
 ### Plots
 
 **Class methods:**
@@ -134,7 +152,8 @@ compare(data,
 
 **Individual functions:**
 - `plot_pca()`, `plot_distributions()`, `plot_missingness()`
-- `plot_volcano()`, `plot_heatmap()`, `plot_upset()`, `plot_pvalue_hist()`, `plot_fc_distribution()`
+- `plot_volcano()`, `plot_heatmap()`, `plot_pvalue_hist()`, `plot_fc_distribution()`
+- `plot_fit_diagnostics()` - GLM model fit assessment
 
 ## File Structure
 
@@ -146,6 +165,7 @@ R/
   tests.R           # Pairwise statistical tests (wilcoxon, bootstrap_t, etc.)
   results.R         # pepdiff_results class, print/summary methods
   plots.R           # All plot functions and plot methods
+  diagnostics.R     # plot_fit_diagnostics() and helpers
   utils.R           # Helpers, validation, internal utilities
   legacy.R          # Deprecated compare.data.frame method
   legacy-pepdiff.R  # Original v1 functions (preserved for compatibility)
@@ -158,7 +178,16 @@ tests/testthat/
   test-tests.R      # Statistical test implementations
   test-results.R    # Results class tests
   test-plots.R      # Plot output tests
+  test-diagnostics.R # Diagnostics function tests
   test-legacy.R     # Backwards compatibility tests
+
+vignettes/
+  basic_workflow.Rmd   # Getting started guide
+  glm_analysis.Rmd     # GLM method deep dive
+  art_analysis.Rmd     # ART method guide
+  pairwise_tests.Rmd   # Pairwise comparison methods
+  checking_fit.Rmd     # GLM diagnostics guide
+  diagnostic_plots.Rmd # Visualization options
 ```
 
 ## Error Handling
@@ -168,7 +197,7 @@ tests/testthat/
 If GLM/ART doesn't converge for a peptide:
 - Peptide excluded from results
 - Tracked in `diagnostics` slot
-- Warning in `print()`: "⚠ X peptides excluded (model did not converge)"
+- Warning in `print()`: "X peptides excluded (model did not converge)"
 
 **Philosophy:** Fail is fail. User needs to know they may need a different design.
 
@@ -188,72 +217,16 @@ Benjamini-Hochberg applied **within each comparison**, not globally across all c
 - Explicit namespace calls for non-base functions (`dplyr::filter()`)
 - Keep test implementations in sync with peppwR (wilcoxon, bootstrap_t, bayes_t, rankprod)
 
-### Development Workflow
-
-We use the **Discuss → TDD → Ralph Loop** workflow. See `semi-autonomous-feature-development.md` for details.
-
-**Summary:**
-1. **Discuss**: Reach shared understanding of the task/feature
-2. **TDD**: Write failing test that captures the requirement, commit it
-3. **Clear Context**: `/clear` or new session to maximize implementation context
-4. **Ralph Loop**: Autonomous implementation with self-contained prompt
-5. **Smoke Test**: Human final verification
-
-### Ralph Loop Prompt Template
-
-```
-/ralph-loop "Implement [feature] for pepdiff.
-
-## Failing Test
-tests/testthat/test-[feature].R
-
-## Relevant Files
-- R/[file].R
-- [other files]
-
-## Verification
-Rscript -e 'devtools::test(filter = "[feature]")'
-Must show: OK
-
-## Success Criteria
-All tests pass, devtools::check() has 0 errors." --completion-promise "FEATURE-COMPLETE" --max-iterations 20
-```
-
-### Key Principles
-
-- **Tests are the contract**: No ambiguity about completion
-- **Small tasks**: Better speed and accuracy than large tasks
-- **Context in files**: Specs live in test files, not conversation history
-- **Clear before execute**: Maximize context for implementation work
-
-## Package Checks
-
-### Routine Development (fast)
-
-Skip vignettes during routine checks:
+### Package Checks
 
 ```r
+# Fast check (skip vignettes)
 devtools::check(vignettes = FALSE)
-```
 
-Or from command line:
-
-```bash
-Rscript -e "devtools::check(vignettes = FALSE)"
-```
-
-### Run Tests Only
-
-```r
+# Run tests only
 devtools::test()
-# Or specific test file:
-devtools::test(filter = "compare")
-```
-
-### Full Check (before release)
 
-```r
-devtools::build_vignettes()
+# Full check
 devtools::check()
 ```
 
@@ -264,10 +237,10 @@ devtools::check()
 - readr - CSV import
 - ggplot2, cowplot - core plotting
 - emmeans - GLM contrast extraction
+- ARTool - ART method
 - stringr, forcats - string/factor utilities
 
 ### Suggests
-- ARTool - ART method
 - ComplexHeatmap - heatmaps (Bioconductor)
 - RankProd - rank products (Bioconductor)
 - UpSetR - upset plots
@@ -276,9 +249,3 @@ devtools::check()
 - knitr, rmarkdown - vignettes
 
 Note: bayes_t uses a native JZS approximation (no BayesFactor dependency)
-
----
-
-## Reference
-
-Full specification: `pepdiff_v2_spec.md`