Convert internal documentation links to repository-relative paths

CONTRIBUTING.md

@@ -5,7 +5,7 @@ Update deterministic tests and documentation when model behavior or result
 fields change.
 
 Use the installation and dependency commands in the
-[README](https://github.com/FritscheLab/phewasFlow#development), reinstall the
+[README](README.md#development), reinstall the
 current source so parallel workers use it, then run:
 
 ```r

README.md

@@ -32,7 +32,7 @@ phewasflow --help
 ```
 
 The R functions work without adding the command-line wrapper to `PATH`.
-For an optional conda environment using [environment.yml](https://github.com/FritscheLab/phewasFlow/blob/main/environment.yml):
+For an optional conda environment using [environment.yml](environment.yml):
 
 ```bash
 mamba env create --file environment.yml
@@ -118,8 +118,9 @@ Phenotypes should already implement the intended observation window,
 case/control definition, and exclusions; `phewasFlow` fits models but does not
 derive phenotypes from raw clinical codes.
 
-The [real-data workflow](https://fritschelab.github.io/phewasFlow/articles/real-data-workflow.html) gives the complete
-participant-table and metadata requirements with working examples.
+The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) documents
+the participant-table and metadata requirements with source examples; for the
+formatted walkthrough, see the [rendered article](https://fritschelab.github.io/phewasFlow/articles/real-data-workflow.html).
 
 ## Validate and run
 
@@ -135,7 +136,7 @@ For a modest analysis, the generated runner performs every stage:
 Rscript run-local.R analysis-forward.yml
 ```
 
-For larger scans, use the [SLURM templates](https://github.com/FritscheLab/phewasFlow/tree/main/inst/examples/slurm) after
+For larger scans, use the [SLURM templates](inst/examples/slurm/) after
 the same analysis succeeds locally on a representative phenotype set.
 
 ## Review the results
@@ -162,13 +163,13 @@ Completed matching shards are reusable after an interrupted run. Change the
 `analysis_id` and output directory whenever the data, model, thresholds, shard
 count, or package version changes.
 
-## Learn more
+## Vignette sources
 
-- [Run a PheWAS with your data](https://fritschelab.github.io/phewasFlow/articles/real-data-workflow.html)
-- [PheWAS in both directions](https://fritschelab.github.io/phewasFlow/articles/two-directions.html)
-- [Comparisons and plots](https://fritschelab.github.io/phewasFlow/articles/comparisons-and-plots.html)
-- [Scale a successful PheWAS](https://fritschelab.github.io/phewasFlow/articles/large-runs.html)
-- [Run a sharded PheWAS with SLURM](https://github.com/FritscheLab/phewasFlow/tree/main/inst/examples/slurm)
+- [Run a PheWAS with your data](vignettes/real-data-workflow.Rmd)
+- [PheWAS in both directions](vignettes/two-directions.Rmd)
+- [Comparisons and plots](vignettes/comparisons-and-plots.Rmd)
+- [Scale a successful PheWAS](vignettes/large-runs.Rmd)
+- [Run a sharded PheWAS with SLURM](inst/examples/slurm/)
 
 ## Development