Point CI, badge, and docs at renamed default branch main

The default branch was renamed Modelling2R6 -> main. Update the push/PR
branch filters in r.yaml and pkgdown.yaml so CI and the pkgdown site keep
triggering, the codecov badge branch, and the 'active development branch'
note in CLAUDE.md/AGENTS.md.

Author: wolski

.github/workflows/pkgdown.yaml

@@ -2,7 +2,7 @@ name: pkgdown
 
 on:
   push:
-    branches: [ Modelling2R6 ]
+    branches: [ main ]
   workflow_dispatch:
 
 permissions:

.github/workflows/r.yaml

@@ -2,9 +2,9 @@ name: R-CMD-check-prolfqua
 
 on:
   push:
-    branches: [ Modelling2R6 ]
+    branches: [ main ]
   pull_request:
-    branches: [ Modelling2R6 ]
+    branches: [ main ]
 
 jobs:
   R-CMD-check:

AGENTS.md

@@ -4,7 +4,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## What is prolfqua
 
-An R package for mass spectrometry-based label-free quantification (LFQ) proteomics analysis. It provides a complete workflow: QC, normalization, protein aggregation, statistical modelling, hypothesis testing, and sample size estimation. Data is always in long (tidy) format. Branch `Modelling2R6` is the active development branch.
+An R package for mass spectrometry-based label-free quantification (LFQ) proteomics analysis. It provides a complete workflow: QC, normalization, protein aggregation, statistical modelling, hypothesis testing, and sample size estimation. Data is always in long (tidy) format. Branch `main` is the active development branch.
 
 ## Build & Test Commands
 

CLAUDE.md

@@ -4,7 +4,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## What is prolfqua
 
-An R package for mass spectrometry-based label-free quantification (LFQ) proteomics analysis. It provides a complete workflow: QC, normalization, protein aggregation, statistical modelling, hypothesis testing, and sample size estimation. Data is always in long (tidy) format. Branch `Modelling2R6` is the active development branch.
+An R package for mass spectrometry-based label-free quantification (LFQ) proteomics analysis. It provides a complete workflow: QC, normalization, protein aggregation, statistical modelling, hypothesis testing, and sample size estimation. Data is always in long (tidy) format. Branch `main` is the active development branch.
 
 ## Build & Test Commands
 

README.md

@@ -1,5 +1,5 @@
 [![R-CMD-check-prolfqua](https://github.com/fgcz/prolfqua/actions/workflows/r.yaml/badge.svg)](https://github.com/fgcz/prolfqua/actions/workflows/r.yaml) ![ReleseeDownloads](https://img.shields.io/github/downloads/fgcz/prolfqua/total)
-[![codecov](https://codecov.io/gh/fgcz/prolfqua/branch/Modelling2R6/graph/badge.svg?token=NP7IPP323C)](https://app.codecov.io/gh/fgcz/prolfqua)
+[![codecov](https://codecov.io/gh/fgcz/prolfqua/branch/main/graph/badge.svg?token=NP7IPP323C)](https://app.codecov.io/gh/fgcz/prolfqua)
 [![DOI](https://img.shields.io/badge/DOI-10.1021%2Facs.jproteome.2c00441-blue)](https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00441)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18775726.svg)](https://doi.org/10.5281/zenodo.18775726)