diff --git a/.github/workflows/end-to-end.yml b/.github/workflows/end-to-end.yml
new file mode 100644
index 000000000..b01257602
--- /dev/null
+++ b/.github/workflows/end-to-end.yml
@@ -0,0 +1,76 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: end-2-end
+
+jobs:
+  end-2-end:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: r-lib/actions/setup-r@v1
+      
+      - uses: actions/checkout@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran('yaml')
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+      
+      - name: Prepare pre-commit
+        run: |
+          config_name <- ".pre-commit-config.yaml"
+          ref_config <- file.path("tests", "testthat", "reference-objects", config_name)
+          len_declared <- length(yaml::read_yaml(".pre-commit-hooks.yaml"))
+          len_testing <- length(yaml::read_yaml(ref_config)$repos[[1]]$hooks)
+          if (len_declared != len_testing) {
+            rlang::abort("You don't test all hooks. Add them to `test_path('reference-objects/.pre-commit-config.yaml')`")
+          }
+          fs::file_delete(config_name)
+          fs::file_copy(ref_config, config_name)
+        shell: Rscript {0}
+      - name: Update Hook revision to current push
+        run: |
+          # hacky, maybe can use pre-commit try-repo?
+          # https://stackoverflow.com/questions/30871868/sed-replace-first-occurence-in-place-with-big-files
+          sed -i ''  -e "1,/rev:.*/{s/rev:.*/rev: $GITHUB_SHA/;}" .pre-commit-config.yaml
+
+      - name: Run pre-commit
+        run: | 
+          echo 'one' >> README.Rmd
+          echo 'one' >> codemeta.json
+          echo 'one' >> README.md
+          echo "#' some code\n#'\n#' @param here.\n#' @name somethings\nNULL" > R/test.R # overwrite if anything there
+          brew install pre-commit
+          pre-commit install
+          pre-commit run --files R/test.R 
+          pre-commit run --files DESCRIPTION 
+          git add README*
+          pre-commit run --files README.Rmd
+          git reset HEAD --hard # restore initial state
+        env:
+          SKIP: consistent-release-tag
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1291701d8..d9519e445 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -39,7 +39,7 @@ repos:
           (.*/|)WORDLIST|
           \.github/workflows/.*|
           data/.*|
-          inst/bin/.*|
+          inst/hooks/.*|
           inst/pre-commit-.*|
           )$
     -   id: readme-rmd-rendered
@@ -56,17 +56,17 @@ repos:
     hooks:
     -   id: consistent-release-tag
         name: consistent-release-tag
-        entry: inst/consistent-release-tag
+        entry: inst/hooks/local/consistent-release-tag.R
         language: script
         stages: [commit, push]
     -   id: hooks-config-to-inst
         name: hooks-config-to-inst
-        entry: inst/hooks-config-to-inst
+        entry: inst/hooks/local/hooks-config-to-inst.R
         language: script
         stages: [commit, push]
     -   id: spell-check-exclude-to-config
         name: spell-check-exclude-to-config
-        entry: inst/spell-check-exclude-to-config
+        entry: inst/hooks/local/spell-check-exclude-to-config.R
         language: script
         stages: [commit, push]
     -   id: forbid-to-commit
@@ -78,6 +78,6 @@ repos:
     -   id: spell-check-ordered-exclude
         name: Ordered regex pattern for spell-check exclusion
         description: Ensure alphabetical order in `exclude:` key of spell check.
-        entry: inst/spell-check-ordered-exclude.R
+        entry: inst/hooks/local/spell-check-ordered-exclude.R
         language: script
         files: '^(.*/|)\.?pre-commit-config.*\.yaml$'
diff --git a/.pre-commit-hooks.yaml b/.pre-commit-hooks.yaml
index c984df30b..a5b3c41d3 100644
--- a/.pre-commit-hooks.yaml
+++ b/.pre-commit-hooks.yaml
@@ -1,7 +1,7 @@
 -   id: roxygenize
     name: roxygenize
     description: run roxygen2::roxygenize()
-    entry: inst/bin/roxygenize
+    entry: inst/hooks/exported/roxygenize.R
     language: script
     files: '^(R|man)/'
     require_serial: true
@@ -9,14 +9,14 @@
 -   id: use-tidy-description
     name: use-tidy-description
     description: run usethis::use_tidy_description()
-    entry: inst/bin/use-tidy-description
+    entry: inst/hooks/exported/use-tidy-description.R
     language: script
     files: '^DESCRIPTION$'
     minimum_pre_commit_version: "2.13.0"
 -   id: style-files
     name: style-files
     description: style files with styler
-    entry: inst/bin/style-files
+    entry: inst/hooks/exported/style-files.R
     language: script
     files: '(\.R|\.Rmd|\.Rnw|\.r|\.rmd|\.rnw)$'
     exclude: 'renv/activate\.R'
@@ -24,35 +24,35 @@
 -   id: no-browser-statement
     name: no-browser-statement
     description: check if a .R file contains a `browser()` statement
-    entry: inst/bin/no-browser-statement
+    entry: inst/hooks/exported/no-browser-statement.R
     language: script
     files: '\.[rR]$'
     minimum_pre_commit_version: "2.13.0"
 -   id: parsable-R
     name: parsable-R
     description: check if a .R file is parsable
-    entry: inst/bin/parsable-R
+    entry: inst/hooks/exported/parsable-R.R
     language: script
     files: '\.[rR]$'
     minimum_pre_commit_version: "2.13.0"
 -   id: readme-rmd-rendered
     name: readme-rmd-rendered
     description: make sure README.Rmd hasn't been edited more recently than README.md
-    entry: inst/bin/readme-rmd-rendered
+    entry: inst/hooks/exported/readme-rmd-rendered
     language: script
     files: 'README\.[Rr]?md$'
     minimum_pre_commit_version: "2.13.0"
 -   id: codemeta-description-updated
     name: codemeta-description-updated
     description: make sure codemeta.json is in sync with DESCRIPTION. It should be run after use-tidy-description.
-    entry: inst/bin/codemeta-description-updated
+    entry: inst/hooks/exported/codemeta-description-updated
     language: script
     files: '^DESCRIPTION$'
     minimum_pre_commit_version: "2.13.0"
 -   id: spell-check 
     name: spell-check
     description: perform a spell check with spelling::spell_check_files()
-    entry: inst/bin/spell-check
+    entry: inst/hooks/exported/spell-check.R
     language: script
     exclude: >
       (?x)^(
@@ -86,7 +86,7 @@
 -   id: deps-in-desc
     name: deps-in-desc
     description: Check if dependencies that can be parsed from code are in DESCRIPTION.
-    entry: inst/bin/deps-in-desc
+    entry: inst/hooks/exported/deps-in-desc.R
     language: script
     files: '(\.[rR]profile|\.R|\.Rmd|\.Rnw|\.r|\.rmd|\.rnw)$'
     exclude: 'renv/activate\.R'
@@ -94,7 +94,7 @@
 -   id: lintr
     name: lintr
     description: check if a .R file is lint free (using lintr)
-    entry: inst/bin/lintr
+    entry: inst/hooks/exported/lintr.R
     language: script
     files: '\.[rR]$'
     exclude: 'renv/activate\.R'
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 5f555abd0..26c961fa3 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -8,7 +8,7 @@ This repo uses the [tic](https://github.com/ropenscilabs/tic) package for CI.
 
 To create a new hook, have a look at the [official
 documentation](https://pre-commit.com/#new-hooks) on creating new hooks, then have a look
-at existing hooks in this repo. The actual executables are defined in [`inst/bin/`](https://github.com/lorenzwalthert/precommit/tree/master/inst/bin). In
+at existing hooks in this repo. The actual executables are defined in [`inst/hooks/`](https://github.com/lorenzwalthert/precommit/tree/master/inst/hooks). In
 the script, you can expect the passed command line arguments to be all options, 
 finally the files that should be processed with the hook.
 
diff --git a/NEWS.md b/NEWS.md
index 0464ddce3..7d4fca3c8 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -56,6 +56,7 @@ depending on whether or not you previously used pre-commit.
 - The `deps-in-desc` hook now points to the hook argument 
   `--allow_private_imports` when the hook fails due to private imports (#254).
 - roxygenize hook is now fully tested (#267).
+- Hook scripts were relocated and R hooks now have a file extension (#280).
 
 # precommit v0.1.3
 
diff --git a/R/testing.R b/R/testing.R
index 7226fce08..ce34a6d74 100644
--- a/R/testing.R
+++ b/R/testing.R
@@ -16,7 +16,8 @@
 #'   the message we expect. To check changed file content, we set `error_msg` to
 #'   `NA`.
 #'
-#' @param hook_name The name of the hook in `bin/`.
+#' @param hook_name The name of the hook in `inst/hooks/exported/`, without
+#'   file extension.
 #' @param file_name The file to test in `tests/in` (without extension). Can be
 #'   a named vector of length one where the name is the target location relative
 #'   to the temporary location and the value is the source of the file.
@@ -41,10 +42,13 @@ run_test <- function(hook_name,
                      artifacts = NULL,
                      file_transformer = function(files) files,
                      env = character()) {
-  path_executable <- system.file(
-    fs::path("bin", hook_name),
+  path_executable <- fs::dir_ls(system.file(
+    fs::path("hooks", "exported"),
     package = "precommit"
-  )
+  ), regexp = paste0("/", hook_name))
+  if (length(path_executable) != 1) {
+    rlang::abort("Failed to derive hook path")
+  }
   path_candidate <- paste0(testthat::test_path("in", file_name), suffix) %>%
     ensure_named(names(file_name), fs::path_file)
   run_test_impl(
diff --git a/inst/WORDLIST b/inst/WORDLIST
index b8752d708..360800d12 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -123,6 +123,7 @@ RStudio
 rstudioapi
 saveCache
 seealso
+SHA
 stderr
 stdout
 sterr
diff --git a/inst/bin/codemeta-description-updated b/inst/hooks/exported/codemeta-description-updated
similarity index 73%
rename from inst/bin/codemeta-description-updated
rename to inst/hooks/exported/codemeta-description-updated
index 884478656..fc692923e 100755
--- a/inst/bin/codemeta-description-updated
+++ b/inst/hooks/exported/codemeta-description-updated
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# adapted from https://github.com/lorenzwalthert/precommit/blob/f4413cfe6282c84f7176160d06e1560860c8bd3d/inst/bin/readme-rmd-rendered
+# adapted from https://github.com/lorenzwalthert/precommit/blob/f4413cfe6282c84f7176160d06e1560860c8bd3d/inst/hooks/exported/readme-rmd-rendered
 
 if [[ DESCRIPTION -nt codemeta.json ]]
 then
diff --git a/inst/bin/deps-in-desc b/inst/hooks/exported/deps-in-desc.R
similarity index 91%
rename from inst/bin/deps-in-desc
rename to inst/hooks/exported/deps-in-desc.R
index 157b3e4a0..98349499b 100755
--- a/inst/bin/deps-in-desc
+++ b/inst/hooks/exported/deps-in-desc.R
@@ -1,12 +1,12 @@
 #!/usr/bin/env Rscript
 
-'Ensure all dependencies of the form pkg::fun are in DESCRIPTION
+"Ensure all dependencies of the form pkg::fun are in DESCRIPTION
 Usage:
   deps-in-desc [--allow_private_imports] <files>...
 
 Options:
   --allow_private_imports  Whether or not to allow the use of ::: on imported functions.
-' -> doc
+" -> doc
 pre_installed <- c(
   "base", "boot", "class", "cluster", "codetools", "compiler",
   "datasets", "foreign", "graphics", "grDevices", "grid", "KernSmooth",
@@ -32,8 +32,8 @@ deps_in_desc <- function(file, arguments) {
     cat(
       "Not all packages used in your code are listed in DESCRIPTION. ",
       "The following are missing in file `", file, "`: ",
-      paste(unregistered, collapse = ", "), ".\n", 
-      "You can add them with `usethis::use_package()` or ", 
+      paste(unregistered, collapse = ", "), ".\n",
+      "You can add them with `usethis::use_package()` or ",
       "`usethis::use_dev_package()`.\n",
       sep = ""
     )
@@ -53,10 +53,10 @@ deps_in_desc <- function(file, arguments) {
       paste0(file, collapse = ", "), "\n\n",
       "If you still think `:::` is a good idea, you can ",
       "allow private imports in your `.pre-commit-config.yaml` like this:
-      
+
     -   id: deps-in-desc
         args: [--allow_private_imports]
-        
+
       ",
       sep = ""
     )
diff --git a/inst/bin/lintr b/inst/hooks/exported/lintr.R
similarity index 100%
rename from inst/bin/lintr
rename to inst/hooks/exported/lintr.R
diff --git a/inst/bin/no-browser-statement b/inst/hooks/exported/no-browser-statement.R
similarity index 84%
rename from inst/bin/no-browser-statement
rename to inst/hooks/exported/no-browser-statement.R
index 43cfd661a..88dcebd18 100755
--- a/inst/bin/no-browser-statement
+++ b/inst/hooks/exported/no-browser-statement.R
@@ -2,10 +2,10 @@
 
 files <- commandArgs(trailing = TRUE)
 no_browser_statement <- function(path) {
-  pd <- getParseData(parse(path,  keep.source = TRUE))
+  pd <- getParseData(parse(path, keep.source = TRUE))
   if (any(pd$text[pd$token == "SYMBOL_FUNCTION_CALL"] == "browser")) {
     stop("File `", path, "` contains a `browser()` statement.", call. = FALSE)
-  } 
+  }
 }
 
 for (file in files) {
diff --git a/inst/bin/parsable-R b/inst/hooks/exported/parsable-R.R
similarity index 91%
rename from inst/bin/parsable-R
rename to inst/hooks/exported/parsable-R.R
index 54858fd37..ae2c1a997 100755
--- a/inst/bin/parsable-R
+++ b/inst/hooks/exported/parsable-R.R
@@ -3,7 +3,7 @@ files <- commandArgs(trailing = TRUE)
 
 out <- lapply(files, function(path) {
   tryCatch(
-    parse(path), 
+    parse(path),
     error = function(x) stop("File ", path, " is not parsable", call. = FALSE)
   )
 })
diff --git a/inst/bin/readme-rmd-rendered b/inst/hooks/exported/readme-rmd-rendered
similarity index 100%
rename from inst/bin/readme-rmd-rendered
rename to inst/hooks/exported/readme-rmd-rendered
diff --git a/inst/bin/roxygenize b/inst/hooks/exported/roxygenize.R
similarity index 100%
rename from inst/bin/roxygenize
rename to inst/hooks/exported/roxygenize.R
diff --git a/inst/bin/spell-check b/inst/hooks/exported/spell-check.R
similarity index 88%
rename from inst/bin/spell-check
rename to inst/hooks/exported/spell-check.R
index df7e4ee22..ec8416e21 100755
--- a/inst/bin/spell-check
+++ b/inst/hooks/exported/spell-check.R
@@ -1,13 +1,13 @@
 #!/usr/bin/env Rscript
 
-'Spell check for files
+"Spell check for files
 Usage:
   spell-check [--lang=<language>] <files>...
 
 Options:
   --lang=<language> Passed to `spelling::spell_check_files()` [default: en_US]
 
-' -> doc
+" -> doc
 
 arguments <- docopt::docopt(doc)
 path_wordlist <- file.path("inst", "WORDLIST")
@@ -26,23 +26,23 @@ if (file.exists(path_wordlist)) {
 
 
 spelling_errors <- spelling::spell_check_files(
-  files, 
-  ignore = ignore, 
+  files,
+  ignore = ignore,
   lang = arguments$lang
 )
 
 if (nrow(spelling_errors) > 0) {
-  cat("The following spelling errors were found:\n" )
+  cat("The following spelling errors were found:\n")
   print(spelling_errors)
   ignore <- sort(unique(c(ignore, spelling_errors$word)))
   ignore <- ignore[ignore != ""] # drop blanks if any
   writeLines(ignore, path_wordlist)
   cat(
-    "All spelling errors found were copied to inst/WORDLIST assuming they were", 
-    "not spelling errors and will be ignored in the future. Please ", 
-    "review the above list and for each word that is an actual typo:\n", 
+    "All spelling errors found were copied to inst/WORDLIST assuming they were",
+    "not spelling errors and will be ignored in the future. Please ",
+    "review the above list and for each word that is an actual typo:\n",
     "- fix it in the source code.\n",
-    "- remove it again manually from inst/WORDLIST to make sure it's not\n", 
+    "- remove it again manually from inst/WORDLIST to make sure it's not\n",
     "  ignored in the future.\n",
     "Then, try committing again.\n"
   )
diff --git a/inst/bin/style-files b/inst/hooks/exported/style-files.R
similarity index 97%
rename from inst/bin/style-files
rename to inst/hooks/exported/style-files.R
index c0f208b71..30bf0b1db 100755
--- a/inst/bin/style-files
+++ b/inst/hooks/exported/style-files.R
@@ -71,7 +71,7 @@ tryCatch(
   },
   warning = function(w) {
     msg <- conditionMessage(w)
-    if (grepl('Unknown or uninitialised column', msg, ignore.case = TRUE)) {
+    if (grepl("Unknown or uninitialised column", msg, ignore.case = TRUE)) {
       warning(msg, call. = FALSE)
     } else {
       stop(msg, call. = FALSE)
diff --git a/inst/bin/use-tidy-description b/inst/hooks/exported/use-tidy-description.R
similarity index 100%
rename from inst/bin/use-tidy-description
rename to inst/hooks/exported/use-tidy-description.R
diff --git a/inst/consistent-release-tag b/inst/hooks/local/consistent-release-tag.R
similarity index 85%
rename from inst/consistent-release-tag
rename to inst/hooks/local/consistent-release-tag.R
index f27f2c786..fa98d35bd 100755
--- a/inst/consistent-release-tag
+++ b/inst/hooks/local/consistent-release-tag.R
@@ -1,11 +1,11 @@
 #!/usr/bin/env Rscript
-'This hook checks that all versions in config files and the git tag that
+"This hook checks that all versions in config files and the git tag that
  is used by precommit to clone the repo is identical.
 
 Usage:
   consistent-release-tag [--release-mode] [<files>...]
 
-' -> doc
+" -> doc
 arguments <- docopt::docopt(doc)
 
 
@@ -13,7 +13,7 @@ arguments <- docopt::docopt(doc)
 # is used by precommit to clone the repo is identical.
 # DESCRIPTION is allowed to have higher version because the process is:
 # - release a version e.g. 0.1.0 on CRAN, all example configs should match DESCRIPTION
-# - continue development: Should bump DESCRIPTION to dev, e.g. 0.1.0.9000, 
+# - continue development: Should bump DESCRIPTION to dev, e.g. 0.1.0.9000,
 #   but not git tag or config examples. These should remain at 0.1.0.
 # - release new version on CRAN, make sure all tags correspond to 0.2.0.
 
@@ -25,16 +25,16 @@ path_config <- c(
 
 
 assert_config_has_rev <- function(path_config, latest_tag) {
-  file <- yaml::read_yaml(path_config) 
-  repo <- purrr::map(file$repos, "repo") 
-  
+  file <- yaml::read_yaml(path_config)
+  repo <- purrr::map(file$repos, "repo")
+
   lorenzwalthert_precommit_idx <- which(repo == "https://github.com/lorenzwalthert/precommit")
   stopifnot(length(lorenzwalthert_precommit_idx) == 1)
   rev <- file$repos[[lorenzwalthert_precommit_idx]]$rev
-  
+
   if (latest_tag != rev) {
     rlang::abort(glue::glue(
-      "latest git tag is `{latest_tag}`, but in `{path_config}`, you the  ", 
+      "latest git tag is `{latest_tag}`, but in `{path_config}`, you the  ",
       "revision is set to `{rev}` Please make the two correspond."
     ))
   }
@@ -50,8 +50,8 @@ latest_tag <- get_latest_tag()
 purrr::walk(path_config, assert_config_has_rev, latest_tag = latest_tag)
 latest_tag_without_prefix <- gsub("^v", "", latest_tag)
 
-if (!(latest_tag_without_prefix < desc::desc_get_field('Version'))) {
-  if (latest_tag_without_prefix > desc::desc_get_field('Version')) {
+if (!(latest_tag_without_prefix < desc::desc_get_field("Version"))) {
+  if (latest_tag_without_prefix > desc::desc_get_field("Version")) {
     rlang::abort(paste(
       "git tag should never be greater than description. At most they should",
       "be equal."
@@ -60,8 +60,6 @@ if (!(latest_tag_without_prefix < desc::desc_get_field('Version'))) {
     rlang::abort(paste(
       "DESCRIPTION version must be larger than git tag unless the check is",
       " performed during a release. Then turn this off with --release-mode"
-      
     ))
   }
-  
 }
diff --git a/inst/hooks-config-to-inst b/inst/hooks/local/hooks-config-to-inst.R
similarity index 80%
rename from inst/hooks-config-to-inst
rename to inst/hooks/local/hooks-config-to-inst.R
index 411566a14..980dfa580 100755
--- a/inst/hooks-config-to-inst
+++ b/inst/hooks/local/hooks-config-to-inst.R
@@ -1,9 +1,10 @@
 #!/usr/bin/env Rscript
 
-# because we need access of .pre-commit-hooks.yaml in the vignette 
+# because we need access of .pre-commit-hooks.yaml in the vignette
 # available-hooks and maybe more general in other places, we must put this
 # file under inst/ because otherwise it cannot be accessed (leaving it on top
 # level will fail r cmd check, the same when used as hidden file in inst/)
 fs::file_copy(
-  ".pre-commit-hooks.yaml", "inst/pre-commit-hooks.yaml", overwrite = TRUE
+  ".pre-commit-hooks.yaml", "inst/pre-commit-hooks.yaml",
+  overwrite = TRUE
 )
diff --git a/inst/spell-check-exclude-to-config b/inst/hooks/local/spell-check-exclude-to-config.R
similarity index 84%
rename from inst/spell-check-exclude-to-config
rename to inst/hooks/local/spell-check-exclude-to-config.R
index 7272ae752..41f026438 100755
--- a/inst/spell-check-exclude-to-config
+++ b/inst/hooks/local/spell-check-exclude-to-config.R
@@ -3,27 +3,27 @@ library(magrittr)
 exclude_hooks <- yaml::read_yaml(here::here(".pre-commit-hooks.yaml")) %>%
   purrr::keep(~ .x$id == "spell-check") %>%
   magrittr::extract2(1) %>%
-  purrr::pluck('exclude')
+  purrr::pluck("exclude")
 
 read_config <- function(path) {
   yaml::read_yaml(path) %>%
-    purrr::pluck('repos') %>%
+    purrr::pluck("repos") %>%
     purrr::keep(~ .x$repo == "https://github.com/lorenzwalthert/precommit") %>%
     purrr::pluck(1, "hooks") %>%
     purrr::keep(~ .x$id == "spell-check") %>%
-    purrr::pluck(1, 'exclude')
+    purrr::pluck(1, "exclude")
 }
 
 if (!identical(exclude_hooks, read_config(here::here("inst/pre-commit-config-pkg.yaml")))) {
   rlang::abort(paste0(
-    "The `exclude` key from the spell-check hook should be copied from `.pre-commit-hooks.yaml` to ", 
+    "The `exclude` key from the spell-check hook should be copied from `.pre-commit-hooks.yaml` to ",
     "`inst/pre-commit-config-pkg.yaml` so the two match."
   ))
 }
 
 if (!identical(exclude_hooks, read_config(here::here("inst/pre-commit-config-proj.yaml")))) {
   rlang::abort(paste0(
-    "The `exclude` key from the spell-check hook should be copied from `.pre-commit-hooks.yaml` to ", 
+    "The `exclude` key from the spell-check hook should be copied from `.pre-commit-hooks.yaml` to ",
     "`inst/pre-commit-config-proj.yaml` so the two match."
   ))
 }
diff --git a/inst/spell-check-ordered-exclude.R b/inst/hooks/local/spell-check-ordered-exclude.R
similarity index 100%
rename from inst/spell-check-ordered-exclude.R
rename to inst/hooks/local/spell-check-ordered-exclude.R
diff --git a/inst/pre-commit-hooks.yaml b/inst/pre-commit-hooks.yaml
index c984df30b..a5b3c41d3 100644
--- a/inst/pre-commit-hooks.yaml
+++ b/inst/pre-commit-hooks.yaml
@@ -1,7 +1,7 @@
 -   id: roxygenize
     name: roxygenize
     description: run roxygen2::roxygenize()
-    entry: inst/bin/roxygenize
+    entry: inst/hooks/exported/roxygenize.R
     language: script
     files: '^(R|man)/'
     require_serial: true
@@ -9,14 +9,14 @@
 -   id: use-tidy-description
     name: use-tidy-description
     description: run usethis::use_tidy_description()
-    entry: inst/bin/use-tidy-description
+    entry: inst/hooks/exported/use-tidy-description.R
     language: script
     files: '^DESCRIPTION$'
     minimum_pre_commit_version: "2.13.0"
 -   id: style-files
     name: style-files
     description: style files with styler
-    entry: inst/bin/style-files
+    entry: inst/hooks/exported/style-files.R
     language: script
     files: '(\.R|\.Rmd|\.Rnw|\.r|\.rmd|\.rnw)$'
     exclude: 'renv/activate\.R'
@@ -24,35 +24,35 @@
 -   id: no-browser-statement
     name: no-browser-statement
     description: check if a .R file contains a `browser()` statement
-    entry: inst/bin/no-browser-statement
+    entry: inst/hooks/exported/no-browser-statement.R
     language: script
     files: '\.[rR]$'
     minimum_pre_commit_version: "2.13.0"
 -   id: parsable-R
     name: parsable-R
     description: check if a .R file is parsable
-    entry: inst/bin/parsable-R
+    entry: inst/hooks/exported/parsable-R.R
     language: script
     files: '\.[rR]$'
     minimum_pre_commit_version: "2.13.0"
 -   id: readme-rmd-rendered
     name: readme-rmd-rendered
     description: make sure README.Rmd hasn't been edited more recently than README.md
-    entry: inst/bin/readme-rmd-rendered
+    entry: inst/hooks/exported/readme-rmd-rendered
     language: script
     files: 'README\.[Rr]?md$'
     minimum_pre_commit_version: "2.13.0"
 -   id: codemeta-description-updated
     name: codemeta-description-updated
     description: make sure codemeta.json is in sync with DESCRIPTION. It should be run after use-tidy-description.
-    entry: inst/bin/codemeta-description-updated
+    entry: inst/hooks/exported/codemeta-description-updated
     language: script
     files: '^DESCRIPTION$'
     minimum_pre_commit_version: "2.13.0"
 -   id: spell-check 
     name: spell-check
     description: perform a spell check with spelling::spell_check_files()
-    entry: inst/bin/spell-check
+    entry: inst/hooks/exported/spell-check.R
     language: script
     exclude: >
       (?x)^(
@@ -86,7 +86,7 @@
 -   id: deps-in-desc
     name: deps-in-desc
     description: Check if dependencies that can be parsed from code are in DESCRIPTION.
-    entry: inst/bin/deps-in-desc
+    entry: inst/hooks/exported/deps-in-desc.R
     language: script
     files: '(\.[rR]profile|\.R|\.Rmd|\.Rnw|\.r|\.rmd|\.rnw)$'
     exclude: 'renv/activate\.R'
@@ -94,7 +94,7 @@
 -   id: lintr
     name: lintr
     description: check if a .R file is lint free (using lintr)
-    entry: inst/bin/lintr
+    entry: inst/hooks/exported/lintr.R
     language: script
     files: '\.[rR]$'
     exclude: 'renv/activate\.R'
diff --git a/man/run_test.Rd b/man/run_test.Rd
index afd74b556..9266f01ca 100644
--- a/man/run_test.Rd
+++ b/man/run_test.Rd
@@ -17,7 +17,8 @@ run_test(
 )
 }
 \arguments{
-\item{hook_name}{The name of the hook in \verb{bin/}.}
+\item{hook_name}{The name of the hook in \verb{inst/hooks/exported/}, without
+file extension.}
 
 \item{file_name}{The file to test in \verb{tests/in} (without extension). Can be
 a named vector of length one where the name is the target location relative
diff --git a/tests/testthat/reference-objects/.pre-commit-config.yaml b/tests/testthat/reference-objects/.pre-commit-config.yaml
new file mode 100644
index 000000000..7c996f30d
--- /dev/null
+++ b/tests/testthat/reference-objects/.pre-commit-config.yaml
@@ -0,0 +1,79 @@
+# config used to run all hooks we have defined in this repo in .github/workflows/end-2-end.yml
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+default_stages: ["commit"]
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.3.9008
+    hooks: 
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]
+        exclude: '^tests/testthat/in/.*\.R'
+    -   id: roxygenize
+    # codemeta must be above use-tidy-description when both are used
+    -   id: codemeta-description-updated
+    -   id: lintr
+    -   id: use-tidy-description
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          .*\.[rR]|
+          .*\.feather|
+          .*\.jpeg|
+          .*\.pdf|
+          .*\.png|
+          .*\.py|
+          .*\.RData|
+          .*\.rds|
+          .*\.Rds|
+          .*\.Rproj|
+          .*\.sh|
+          (.*/|)\.gitignore|
+          (.*/|)\.pre-commit-.*|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.Renviron|
+          (.*/|)\.Rprofile|
+          (.*/|)\.travis\.yml|
+          (.*/|)appveyor\.yml|
+          (.*/|)NAMESPACE|
+          (.*/|)renv/settings\.dcf|
+          (.*/|)renv\.lock|
+          (.*/|)WORDLIST|
+          \.github/workflows/.*|
+          data/.*|
+          inst/hooks/.*|
+          inst/pre-commit-.*|
+          )$
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: deps-in-desc
+-   repo: local
+    hooks:
+    -   id: consistent-release-tag
+        name: consistent-release-tag
+        entry: inst/hooks/local/consistent-release-tag.R
+        language: script
+        stages: [commit, push]
+    -   id: hooks-config-to-inst
+        name: hooks-config-to-inst
+        entry: inst/hooks/local/hooks-config-to-inst.R
+        language: script
+        stages: [commit, push]
+    -   id: spell-check-exclude-to-config
+        name: spell-check-exclude-to-config
+        entry: inst/hooks/local/spell-check-exclude-to-config.R
+        language: script
+        stages: [commit, push]
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .Rdata, .csv and similar.
+        language: fail
+        files: '\.Rhistory|\.csv|\.RData|\.Rds|\.rds$'
+        # `exclude: <regex>` to allow committing specific files.
+    -   id: spell-check-ordered-exclude
+        name: Ordered regex pattern for spell-check exclusion
+        description: Ensure alphabetical order in `exclude:` key of spell check.
+        entry: inst/hooks/local/spell-check-ordered-exclude.R
+        language: script
+        files: '^(.*/|)\.?pre-commit-config.*\.yaml$'
diff --git a/vignettes/testing.Rmd b/vignettes/testing.Rmd
index e75c1b691..8d80bcdf9 100644
--- a/vignettes/testing.Rmd
+++ b/vignettes/testing.Rmd
@@ -18,7 +18,7 @@ pre-commit >= 2.11.0 supports R as a language and each hook repo has its own
 virtual environment with package versions locked. For that reason, we should
 also test with exactly these versions.
 
-This package has four testing workflows:
+This package has five testing workflows:
 
 * hook testing. Tests the hooks (as well as hook script helpers?) in the renv in
   which they'll be shipped. No R CMD Check or pre-commit executable needed.
@@ -48,3 +48,9 @@ This package has four testing workflows:
 
 * CRAN testing. On CRAN, complete testing is ran, tests that check pre-commit
   executable access are disabled.
+
+* end-2-end testing: This simulates closely what happens when you run 
+  `git commit` with pre-commit activated: We update the `.pre-commit-config.yaml` 
+  to the pushed SHA and run `pre-commit run`, covering all hooks, to ensure in 
+  particular file linking, file permissions etc. in `.pre-commit-hooks.yaml` are
+  correct for exported hooks.