# Task A6 Report: Wire patched repo into the pak install path

## Status: COMPLETE

## TDD Evidence

### RED (failing test)
Added the new test to `tests/testthat/test-patches.R` (before the `prepare_patched_repo serves a cached binary` test).
Run output:
```
ERROR: 'test-patches.R:184:3' ---------------------
Error in `run_pak_install_with_mutex(tempfile(), list(), patched_repo = "/tmp/patched")`: unused argument (patched_repo = "/tmp/patched")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 35 ]
```

### GREEN (all pass)
After applying the two file edits:
```
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
```

## Commit

SHA: `e2c74c9`
Subject: `feat(patches): serve patched binaries to pak during dep install`
Branch: `feat/package-patching`
Files changed: 3 (60 insertions, 8 deletions)

## Diff Hunks Applied

### `R/install_helpers.R` — signature expansion + repos-prepend wrapper

```diff
-run_pak_install_with_mutex <- function(local_clone_dir_single, env_vars) {
+run_pak_install_with_mutex <- function(
+  local_clone_dir_single,
+  env_vars,
+  patched_repo = NULL
+) {
```

```diff
-          retry_with_backoff(function() {
-            withr::with_envvar(env_vars, {
-              # Default to non-verbose (suppressed messages)
-              suppressMessages(pak::local_install_deps(sprintf(
-                "%s",
-                local_clone_dir_single
-              )))
-            })
-          })
+          retry_with_backoff(function() {
+            withr::with_envvar(env_vars, {
+              repos <- getOption("repos")
+              if (!is.null(patched_repo)) {
+                repos <- c(
+                  patched = sprintf("file://%s", patched_repo),
+                  repos
+                )
+              }
+              withr::with_options(list(repos = repos), {
+                # Default to non-verbose (suppressed messages)
+                suppressMessages(pak::local_install_deps(sprintf(
+                  "%s",
+                  local_clone_dir_single
+                )))
+              })
+            })
+          })
```

### `R/install-deps.R` — signature expansion + patched_repo block

```diff
 install_pkg_sys_deps <- function(
   package_name,
   tag,
   local_clone_dir,
   platform = platform,
-  aggressive_cleanup = FALSE
+  aggressive_cleanup = FALSE,
+  patches = NULL,
+  arch = NULL
 ) {
```

```diff
+  # Build a local repo of patched binaries (if any apply) and serve it to pak.
+  r_minor <- paste(
+    R.version$major,
+    strsplit(R.version$minor, ".", fixed = TRUE)[[1L]][1L],
+    sep = "."
+  )
+  patched_repo <- tryCatch(
+    prepare_patched_repo(patches, platform, arch, r_minor),
+    error = function(e) {
+      log_warn(sprintf("Patch preparation failed: %s", conditionMessage(e)))
+      NULL
+    }
+  )
+
   # Run installation with mutex protection
   run_pak_install_with_mutex(
     local_clone_dir_single,
-    env_vars
+    env_vars,
+    patched_repo = patched_repo
   )
```

### `tests/testthat/test-patches.R` — new test appended before the cached-binary test

```r
test_that("run_pak_install_with_mutex prepends the patched repo to repos", {
  seen <- NULL
  local_mocked_bindings(
    acquire_pak_mutex = function(...) tempfile(),
    release_pak_mutex = function(...) invisible(NULL),
    retry_with_backoff = function(func, ...) func()
  )
  local_mocked_bindings(
    local_install_deps = function(...) {
      seen <<- getOption("repos")
      invisible(TRUE)
    },
    .package = "pak"
  )

  run_pak_install_with_mutex(
    tempfile(), list(), patched_repo = "/tmp/patched"
  )

  expect_true(any(grepl("file:///tmp/patched", seen)))
})
```

## Concerns

None.
The existing brace-escaping patterns in the error handler of `run_pak_install_with_mutex` were left untouched.
No refactoring was done beyond the specified additions.
`prepare_patched_repo` errors are caught and logged via `log_warn` with `NULL` fallback, so a missing/empty patch registry causes no disruption to existing install flows.