From 70d14e1026292d9310845be37777db95fd20ad23 Mon Sep 17 00:00:00 2001
From: Anderson E <andersone@example.com>
Date: Thu, 18 Dec 2025 09:48:49 -0500
Subject: [PATCH 1/7] v1

---
 R/runWithOutputs.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 R/runWithOutputs.R

diff --git a/R/runWithOutputs.R b/R/runWithOutputs.R
new file mode 100644
index 0000000..dc8e23a
--- /dev/null
+++ b/R/runWithOutputs.R
@@ -0,0 +1,32 @@
+runWithOutputs <- function(script) {
+  root <- here::here()
+
+  # 1. Capture start time to establish a baseline for file modifications
+  t0 <- Sys.time()
+
+  # 2. Execute the script in a fresh R session
+  callr::rscript(script, wd = root)
+
+  # 3. List candidate files using `fd`
+  res <- processx::run(
+    "fd",
+    args = c("--type", "f", "--exclude", "renv"),
+    wd = root
+  )
+
+  if (res$stdout != "") {
+    files <- unlist(strsplit(trimws(res$stdout), "\n"))
+    abs_paths <- fs::path(root, files)
+    changed <- files[file.mtime(abs_paths) > t0]
+
+    # 5. Output results as YAML
+    if (length(changed) > 0) {
+      changed <- sort(changed)
+      yaml_str <- paste0(
+        "outputs:\n",
+        paste0("   - \"", changed, "\"\n", collapse = "")
+      )
+      cli::cli_code(yaml_str)
+    }
+  }
+}

From df6477eb2c00da1b984dd3eb21ed913856435baa Mon Sep 17 00:00:00 2001
From: Anderson E <andersone@example.com>
Date: Thu, 18 Dec 2025 09:58:04 -0500
Subject: [PATCH 2/7] docs

---
 DESCRIPTION                          |  3 +++
 NAMESPACE                            |  1 +
 R/runWithOutputs.R                   | 17 +++++++++++++++++
 man/runWithOutputs.Rd                | 26 ++++++++++++++++++++++++++
 tests/testthat/test-runWithOutputs.R | 27 +++++++++++++++++++++++++++
 5 files changed, 74 insertions(+)
 create mode 100644 man/runWithOutputs.Rd
 create mode 100644 tests/testthat/test-runWithOutputs.R

diff --git a/DESCRIPTION b/DESCRIPTION
index ed5bb9c..24fbad4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,6 +17,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 Imports: 
     dplyr,
+    callr,
     magrittr (>= 2.0.3),
     XML,
     utils,
@@ -25,6 +26,7 @@ Imports:
     stringr,
     fs,
     cli,
+    here,
     rmarkdown,
     tinytex,
     pmtables,
@@ -34,6 +36,7 @@ Imports:
     htmltools,
     shiny,
     pdftools,
+    processx,
     stringi
 Suggests: 
     knitr,
diff --git a/NAMESPACE b/NAMESPACE
index 2cdafe9..b6825d5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -21,6 +21,7 @@ export(logSummary)
 export(renderQCReport)
 export(renderQCSummary)
 export(repoHistory)
+export(runWithOutputs)
 export(svnExport)
 export(svnLog)
 export(with_demoRepo)
diff --git a/R/runWithOutputs.R b/R/runWithOutputs.R
index dc8e23a..318cfc8 100644
--- a/R/runWithOutputs.R
+++ b/R/runWithOutputs.R
@@ -1,3 +1,20 @@
+ #' Run a Script and Report Outputs
+ #'
+ #' Runs an R script from the project root in a clean R session and reports any
+ #' files modified during the run as YAML. Uses `fd` to identify files (excluding
+ #' the `renv` directory) and prints the relative paths for downstream tooling.
+ #'
+#' @param script Path to the script to execute.
+#'
+#' @return Invisibly returns `NULL`; prints YAML of files changed since the
+#'   script started.
+#'
+#' @examples
+#' \dontrun{
+#'   runWithOutputs("path/to/script.R")
+#' }
+#'
+#' @export
 runWithOutputs <- function(script) {
   root <- here::here()
 
diff --git a/man/runWithOutputs.Rd b/man/runWithOutputs.Rd
new file mode 100644
index 0000000..a49d82a
--- /dev/null
+++ b/man/runWithOutputs.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runWithOutputs.R
+\name{runWithOutputs}
+\alias{runWithOutputs}
+\title{Run a Script and Report Outputs}
+\usage{
+runWithOutputs(script)
+}
+\arguments{
+\item{script}{Path to the script to execute.}
+}
+\value{
+Invisibly returns \code{NULL}; prints YAML of files changed since the
+script started.
+}
+\description{
+Runs an R script from the project root in a clean R session and reports any
+files modified during the run as YAML. Uses \code{fd} to identify files (excluding
+the \code{renv} directory) and prints the relative paths for downstream tooling.
+}
+\examples{
+\dontrun{
+  runWithOutputs("path/to/script.R")
+}
+
+}
diff --git a/tests/testthat/test-runWithOutputs.R b/tests/testthat/test-runWithOutputs.R
new file mode 100644
index 0000000..804648e
--- /dev/null
+++ b/tests/testthat/test-runWithOutputs.R
@@ -0,0 +1,27 @@
+# Tests for runWithOutputs
+
+test_that("runWithOutputs reports newly created files", {
+  skip_if(Sys.which("fd") == "", "fd command not available")
+
+  root <- here::here()
+  tmp_dir <- file.path(root, "tmp_runWithOutputs")
+  dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE)
+  withr::defer(unlink(tmp_dir, recursive = TRUE, force = TRUE))
+
+  artifact <- file.path(tmp_dir, "artifact.txt")
+  script <- file.path(tmp_dir, "make_artifact.R")
+
+  writeLines(
+    c(
+      "Sys.sleep(0.1)",
+      sprintf("writeLines('test output', '%s')", artifact)
+    ),
+    script
+  )
+
+  out <- testthat::capture_output(runWithOutputs(script))
+
+  expect_true(file.exists(artifact))
+  expect_match(out, "outputs:")
+  expect_match(out, "tmp_runWithOutputs/artifact.txt")
+})

From ee3a708b2af825e3948439d2ca1ac6251e647c9b Mon Sep 17 00:00:00 2001
From: anderson <andersone@metrumrg.com>
Date: Thu, 18 Dec 2025 11:46:24 -0500
Subject: [PATCH 3/7] fix tests

---
 DESCRIPTION                          |   4 +-
 R/reviewPackage.R                    |   5 +-
 R/runWithOutputs.R                   | 107 +++++++++++++-------
 man/runWithOutputs.Rd                |  22 ++--
 tests/testthat/test-runWithOutputs.R | 144 +++++++++++++++++++++++----
 5 files changed, 208 insertions(+), 74 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 24fbad4..d17c9be 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,8 +36,8 @@ Imports:
     htmltools,
     shiny,
     pdftools,
-    processx,
-    stringi
+    stringi,
+    yaml
 Suggests: 
     knitr,
     testthat (>= 3.0.0),
diff --git a/R/reviewPackage.R b/R/reviewPackage.R
index 0ef8bd9..0024e27 100644
--- a/R/reviewPackage.R
+++ b/R/reviewPackage.R
@@ -29,6 +29,9 @@ globalVariables(
     "path",
     "page",
     "type",
-    "code_path"
+    "code_path",
+    "rel_path",
+    "modification_time",
+    "size"
   )
 )
\ No newline at end of file
diff --git a/R/runWithOutputs.R b/R/runWithOutputs.R
index 318cfc8..d4c1744 100644
--- a/R/runWithOutputs.R
+++ b/R/runWithOutputs.R
@@ -1,49 +1,80 @@
- #' Run a Script and Report Outputs
- #'
- #' Runs an R script from the project root in a clean R session and reports any
- #' files modified during the run as YAML. Uses `fd` to identify files (excluding
- #' the `renv` directory) and prints the relative paths for downstream tooling.
- #'
-#' @param script Path to the script to execute.
+#' Run a Script and Report Outputs
 #'
-#' @return Invisibly returns `NULL`; prints YAML of files changed since the
-#'   script started.
+#' Runs an R script from the project root in a clean R session and reports any
+#' files saved (created or updated) during the run.
 #'
-#' @examples
-#' \dontrun{
-#'   runWithOutputs("path/to/script.R")
-#' }
+#' @param script Path to the script to execute.
+#' @param root Path to the project root. Defaults to `here::here()`.
+#' @param exclude_dirs Character vector of directories relative to `root` to ignore.
 #'
+#' @return Invisibly returns a vector of relative paths for changed files.
 #' @export
-runWithOutputs <- function(script) {
-  root <- here::here()
+runWithOutputs <- function(
+  script,
+  root = here::here(),
+  exclude_dirs = c("renv", ".svn", ".git")
+) {
+  # Normalize script path to absolute so callr finds it regardless of 'wd' change
+  script_abs <- fs::path_abs(script)
 
-  # 1. Capture start time to establish a baseline for file modifications
-  t0 <- Sys.time()
+  # Snapshot before
+  # We track size as well to catch changes that might happen within the same second
+  # on low-resolution file systems if the content length changes.
+  before <- fs::dir_info(root, recurse = TRUE, type = "file") %>%
+    dplyr::select(path, modification_time, size)
 
-  # 2. Execute the script in a fresh R session
-  callr::rscript(script, wd = root)
+  # --- Start Header ---
+  div_start <- cli::cli_div(theme = list(rule = list(color = "cyan")))
+  cli::cli_rule(
+    left = cli::style_bold(cli::bg_cyan(cli::col_white(" runWithOutputs() "))),
+    right = "START"
+  )
+  cli::cli_bullets(c(
+    "*" = paste0(cli::style_bold("Script: "), cli::col_blue("{.path {script}}"))
+  ))
+  cli::cli_end(div_start)
 
-  # 3. List candidate files using `fd`
-  res <- processx::run(
-    "fd",
-    args = c("--type", "f", "--exclude", "renv"),
-    wd = root
+  # Execute script
+  # We use callr::rscript to run in a fresh session
+  callr::rscript(script_abs, wd = root, show = TRUE)
+
+  # --- End Header ---
+  div_end <- cli::cli_div(theme = list(rule = list(color = "cyan")))
+  cli::cli_rule(
+    left = cli::style_bold(cli::bg_cyan(cli::col_white(" runWithOutputs() "))),
+    right = "COMPLETE"
   )
+  cli::cli_end(div_end)
+
+  # Snapshot after
+  after <- fs::dir_info(root, recurse = TRUE, type = "file") %>%
+    dplyr::select(path, modification_time, size)
+
+  # Detect changes
+  changed <- dplyr::anti_join(
+    after,
+    before,
+    by = c("path", "modification_time", "size")
+  ) %>%
+    dplyr::mutate(rel_path = fs::path_rel(path, start = root))
+
+  # Filter exclusions using regex
+  if (length(exclude_dirs) > 0) {
+    safe_dirs <- gsub(".", "\\.", exclude_dirs, fixed = TRUE)
+    # Ensure we match directories at the start of the relative path
+    pattern <- paste0("^(", paste(safe_dirs, collapse = "|"), ")/")
+    changed <- dplyr::filter(changed, !grepl(pattern, rel_path))
+  }
+
+  # Output
+  out_paths <- sort(changed$rel_path)
 
-  if (res$stdout != "") {
-    files <- unlist(strsplit(trimws(res$stdout), "\n"))
-    abs_paths <- fs::path(root, files)
-    changed <- files[file.mtime(abs_paths) > t0]
-
-    # 5. Output results as YAML
-    if (length(changed) > 0) {
-      changed <- sort(changed)
-      yaml_str <- paste0(
-        "outputs:\n",
-        paste0("   - \"", changed, "\"\n", collapse = "")
-      )
-      cli::cli_code(yaml_str)
-    }
+  if (length(out_paths) > 0) {
+    cli::cli_alert_success("Files saved by this run:")
+    cli::cli_code(yaml::as.yaml(list(outputs = out_paths)))
+    invisible(out_paths)
+  } else {
+    cli::cli_alert_success(cli::col_silver("No files were saved."))
+    invisible(character(0))
   }
 }
diff --git a/man/runWithOutputs.Rd b/man/runWithOutputs.Rd
index a49d82a..055c0b8 100644
--- a/man/runWithOutputs.Rd
+++ b/man/runWithOutputs.Rd
@@ -4,23 +4,23 @@
 \alias{runWithOutputs}
 \title{Run a Script and Report Outputs}
 \usage{
-runWithOutputs(script)
+runWithOutputs(
+  script,
+  root = here::here(),
+  exclude_dirs = c("renv", ".svn", ".git")
+)
 }
 \arguments{
 \item{script}{Path to the script to execute.}
+
+\item{root}{Path to the project root. Defaults to \code{here::here()}.}
+
+\item{exclude_dirs}{Character vector of directories relative to \code{root} to ignore.}
 }
 \value{
-Invisibly returns \code{NULL}; prints YAML of files changed since the
-script started.
+Invisibly returns a vector of relative paths for changed files.
 }
 \description{
 Runs an R script from the project root in a clean R session and reports any
-files modified during the run as YAML. Uses \code{fd} to identify files (excluding
-the \code{renv} directory) and prints the relative paths for downstream tooling.
-}
-\examples{
-\dontrun{
-  runWithOutputs("path/to/script.R")
-}
-
+files saved (created or updated) during the run.
 }
diff --git a/tests/testthat/test-runWithOutputs.R b/tests/testthat/test-runWithOutputs.R
index 804648e..ba2e5c4 100644
--- a/tests/testthat/test-runWithOutputs.R
+++ b/tests/testthat/test-runWithOutputs.R
@@ -1,27 +1,127 @@
-# Tests for runWithOutputs
-
-test_that("runWithOutputs reports newly created files", {
-  skip_if(Sys.which("fd") == "", "fd command not available")
-
-  root <- here::here()
-  tmp_dir <- file.path(root, "tmp_runWithOutputs")
-  dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE)
-  withr::defer(unlink(tmp_dir, recursive = TRUE, force = TRUE))
+test_that("runWithOutputs detects newly created files", {
+  with_demoRepo({
+    # Setup: Create a script that generates a new output file
+    script_path <- "script/generate_data.R"
+    output_file <- "data/new_result.txt"
+    
+    # using fs::dir_create handles parent dirs and existence checks automatically
+    fs::dir_create("script") 
+    
+    writeLines(
+      text = c(
+        'dir.create("data", showWarnings = FALSE)',
+        paste0('writeLines("content", "', output_file, '")')
+      ),
+      con = script_path
+    )
+    
+    # Execution
+    result <- runWithOutputs(script_path, root = getwd())
+    
+    # Verification: Check return value
+    expect_true(output_file %in% result)
+    # Ensure the script itself is not listed as an output
+    expect_false(script_path %in% result)
+  })
+})
 
-  artifact <- file.path(tmp_dir, "artifact.txt")
-  script <- file.path(tmp_dir, "make_artifact.R")
+test_that("runWithOutputs detects modified files", {
+  with_demoRepo({
+    # Setup: Create an existing file
+    target_file <- "data/existing_file.txt"
+    fs::dir_create("data")
+    writeLines("old content", target_file)
+    
+    # OPTIMIZATION: Manually backdate the file timestamp.
+    # This ensures the test is robust without using Sys.sleep().
+    Sys.setFileTime(target_file, Sys.time() - 60)
+    
+    script_path <- "script/modify_data.R"
+    fs::dir_create("script")
+    
+    writeLines(
+      text = paste0('writeLines("new content", "', target_file, '")'),
+      con = script_path
+    )
+    
+    # Execution
+    result <- runWithOutputs(script_path, root = getwd())
+    
+    # Verification
+    expect_true(target_file %in% result)
+  })
+})
 
-  writeLines(
-    c(
-      "Sys.sleep(0.1)",
-      sprintf("writeLines('test output', '%s')", artifact)
-    ),
-    script
-  )
+test_that("runWithOutputs returns empty vector when no files change", {
+  with_demoRepo({
+    script_path <- "script/do_nothing.R"
+    fs::dir_create("script")
+    writeLines("print('No file changes here')", script_path)
+    
+    # Execution
+    result <- runWithOutputs(script_path, root = getwd())
+    
+    expect_identical(result, character(0))
+  })
+})
 
-  out <- testthat::capture_output(runWithOutputs(script))
+test_that("runWithOutputs respects default excluded directories", {
+  with_demoRepo({
+    # Setup: Create directories
+    fs::dir_create("renv")
+    fs::dir_create("scratch")
+    fs::dir_create("data")
+    fs::dir_create("script")
+    
+    script_path <- "script/mixed_outputs.R"
+    
+    # Script writes to:
+    # 1. renv (should be ignored by DEFAULT exclusion)
+    # 2. scratch (should be included, as it's not a default exclusion)
+    # 3. data (should be included)
+    writeLines(
+      text = c(
+        'writeLines("a", "renv/ignored.txt")',
+        'writeLines("b", "scratch/included.txt")',
+        'writeLines("c", "data/important.txt")'
+      ),
+      con = script_path
+    )
+    
+    # Execution
+    result <- runWithOutputs(script_path, root = getwd())
+    
+    # Verification
+    expect_true("data/important.txt" %in% result)
+    expect_true("scratch/included.txt" %in% result)
+    expect_false("renv/ignored.txt" %in% result)
+  })
+})
 
-  expect_true(file.exists(artifact))
-  expect_match(out, "outputs:")
-  expect_match(out, "tmp_runWithOutputs/artifact.txt")
+test_that("runWithOutputs respects custom excluded directories argument", {
+  with_demoRepo({
+    fs::dir_create("custom_folder")
+    script_path <- "script.R"
+    
+    writeLines('writeLines("x", "custom_folder/file.txt")', script_path)
+    
+    # Pass a custom exclusion list
+    result <- runWithOutputs(
+      script_path, 
+      root = getwd(), 
+      exclude_dirs = c("custom_folder")
+    )
+    
+    expect_false("custom_folder/file.txt" %in% result)
+  })
 })
+
+test_that("runWithOutputs errors if the script execution fails", {
+  with_demoRepo({
+    script_path <- "broken.R"
+    writeLines("stop('Critical error')", script_path)
+    
+    # Verification
+    expect_error(runWithOutputs(script_path, root = getwd()))
+  })
+})
\ No newline at end of file

From e490cb5888bd3a502b46c1a7c042e42dd5a2cef6 Mon Sep 17 00:00:00 2001
From: anderson <andersone@metrumrg.com>
Date: Thu, 18 Dec 2025 12:19:19 -0500
Subject: [PATCH 4/7] docs

---
 DESCRIPTION                          |  3 +-
 R/runWithOutputs.R                   | 68 +++++++++++---------
 man/runWithOutputs.Rd                | 17 ++---
 tests/testthat/test-runWithOutputs.R | 92 +++++++++++++++++-----------
 4 files changed, 107 insertions(+), 73 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d17c9be..f188968 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,7 +37,8 @@ Imports:
     shiny,
     pdftools,
     stringi,
-    yaml
+    yaml,
+    purrr
 Suggests: 
     knitr,
     testthat (>= 3.0.0),
diff --git a/R/runWithOutputs.R b/R/runWithOutputs.R
index d4c1744..6c57134 100644
--- a/R/runWithOutputs.R
+++ b/R/runWithOutputs.R
@@ -1,44 +1,50 @@
-#' Run a Script and Report Outputs
+#' Execute Script and Detect File Changes
 #'
-#' Runs an R script from the project root in a clean R session and reports any
-#' files saved (created or updated) during the run.
+#' Runs an R script in an isolated session and identifies files that were created
+#' or modified during execution. It detects changes by comparing the file system
+#' state (modification time and size) before and after the run.
 #'
-#' @param script Path to the script to execute.
-#' @param root Path to the project root. Defaults to `here::here()`.
-#' @param exclude_dirs Character vector of directories relative to `root` to ignore.
+#' @param script Character. The path to the R script to execute.
+#' @param root Character. The project root directory. Defaults to `here::here()`.
+#' @param exclude_dirs Character vector. A list of top-level directories relative
+#'   to `root` to ignore when scanning for changes (e.g., "renv", ".git").
 #'
-#' @return Invisibly returns a vector of relative paths for changed files.
+#' @return Invisibly returns a character vector of relative paths for all files
+#'   that were created or updated.
 #' @export
 runWithOutputs <- function(
   script,
   root = here::here(),
   exclude_dirs = c("renv", ".svn", ".git")
 ) {
-  # Normalize script path to absolute so callr finds it regardless of 'wd' change
+  # Normalize paths and calculate relative path for the UI
   script_abs <- fs::path_abs(script)
+  script_rel <- fs::path_rel(script_abs, start = root)
 
-  # Snapshot before
-  # We track size as well to catch changes that might happen within the same second
-  # on low-resolution file systems if the content length changes.
+  # 1. Capture Initial State
+  # Define file state by path, modification time, and size.
   before <- fs::dir_info(root, recurse = TRUE, type = "file") %>%
     dplyr::select(path, modification_time, size)
 
-  # --- Start Header ---
+  # --- UI Header ---
+  # Shows the relative path in the badge for immediate context.
   div_start <- cli::cli_div(theme = list(rule = list(color = "cyan")))
   cli::cli_rule(
-    left = cli::style_bold(cli::bg_cyan(cli::col_white(" runWithOutputs() "))),
+    left = cli::style_bold(cli::bg_cyan(cli::col_white(paste0(
+      " runWithOutputs('",
+      script_rel,
+      "') "
+    )))),
     right = "START"
   )
-  cli::cli_bullets(c(
-    "*" = paste0(cli::style_bold("Script: "), cli::col_blue("{.path {script}}"))
-  ))
   cli::cli_end(div_start)
 
-  # Execute script
-  # We use callr::rscript to run in a fresh session
+  # 2. Execute Script
+  # Run in a clean, separate R session to ensure isolation.
   callr::rscript(script_abs, wd = root, show = TRUE)
 
-  # --- End Header ---
+  # --- UI Footer ---
+  # Provides a clean "closing bracket" for the script output.
   div_end <- cli::cli_div(theme = list(rule = list(color = "cyan")))
   cli::cli_rule(
     left = cli::style_bold(cli::bg_cyan(cli::col_white(" runWithOutputs() "))),
@@ -46,11 +52,13 @@ runWithOutputs <- function(
   )
   cli::cli_end(div_end)
 
-  # Snapshot after
+  # 3. Capture Final State
   after <- fs::dir_info(root, recurse = TRUE, type = "file") %>%
     dplyr::select(path, modification_time, size)
 
-  # Detect changes
+  # 4. Compute State Differences
+  # Identify files where the (path, time, size) tuple in the 'after' snapshot
+  # does not strictly match the 'before' snapshot.
   changed <- dplyr::anti_join(
     after,
     before,
@@ -58,15 +66,17 @@ runWithOutputs <- function(
   ) %>%
     dplyr::mutate(rel_path = fs::path_rel(path, start = root))
 
-  # Filter exclusions using regex
-  if (length(exclude_dirs) > 0) {
-    safe_dirs <- gsub(".", "\\.", exclude_dirs, fixed = TRUE)
-    # Ensure we match directories at the start of the relative path
-    pattern <- paste0("^(", paste(safe_dirs, collapse = "|"), ")/")
-    changed <- dplyr::filter(changed, !grepl(pattern, rel_path))
+  # 5. Apply Exclusions
+  # Filter out files where the top-level directory matches an exclusion pattern.
+  if (length(exclude_dirs) > 0 && nrow(changed) > 0) {
+    changed <- changed %>%
+      dplyr::filter(
+        !fs::path_split(rel_path) %>%
+          purrr::map_lgl(~ .x[1] %in% exclude_dirs)
+      )
   }
 
-  # Output
+  # 6. Report Results
   out_paths <- sort(changed$rel_path)
 
   if (length(out_paths) > 0) {
@@ -74,7 +84,7 @@ runWithOutputs <- function(
     cli::cli_code(yaml::as.yaml(list(outputs = out_paths)))
     invisible(out_paths)
   } else {
-    cli::cli_alert_success(cli::col_silver("No files were saved."))
+    cli::cli_alert_info(cli::col_silver("No files were saved."))
     invisible(character(0))
   }
 }
diff --git a/man/runWithOutputs.Rd b/man/runWithOutputs.Rd
index 055c0b8..d8bae77 100644
--- a/man/runWithOutputs.Rd
+++ b/man/runWithOutputs.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/runWithOutputs.R
 \name{runWithOutputs}
 \alias{runWithOutputs}
-\title{Run a Script and Report Outputs}
+\title{Execute Script and Detect File Changes}
 \usage{
 runWithOutputs(
   script,
@@ -11,16 +11,19 @@ runWithOutputs(
 )
 }
 \arguments{
-\item{script}{Path to the script to execute.}
+\item{script}{Character. The path to the R script to execute.}
 
-\item{root}{Path to the project root. Defaults to \code{here::here()}.}
+\item{root}{Character. The project root directory. Defaults to \code{here::here()}.}
 
-\item{exclude_dirs}{Character vector of directories relative to \code{root} to ignore.}
+\item{exclude_dirs}{Character vector. A list of top-level directories relative
+to \code{root} to ignore when scanning for changes (e.g., "renv", ".git").}
 }
 \value{
-Invisibly returns a vector of relative paths for changed files.
+Invisibly returns a character vector of relative paths for all files
+that were created or updated.
 }
 \description{
-Runs an R script from the project root in a clean R session and reports any
-files saved (created or updated) during the run.
+Runs an R script in an isolated session and identifies files that were created
+or modified during execution. It detects changes by comparing the file system
+state (modification time and size) before and after the run.
 }
diff --git a/tests/testthat/test-runWithOutputs.R b/tests/testthat/test-runWithOutputs.R
index ba2e5c4..40d3f6c 100644
--- a/tests/testthat/test-runWithOutputs.R
+++ b/tests/testthat/test-runWithOutputs.R
@@ -3,10 +3,9 @@ test_that("runWithOutputs detects newly created files", {
     # Setup: Create a script that generates a new output file
     script_path <- "script/generate_data.R"
     output_file <- "data/new_result.txt"
-    
-    # using fs::dir_create handles parent dirs and existence checks automatically
-    fs::dir_create("script") 
-    
+
+    fs::dir_create("script")
+
     writeLines(
       text = c(
         'dir.create("data", showWarnings = FALSE)',
@@ -14,14 +13,12 @@ test_that("runWithOutputs detects newly created files", {
       ),
       con = script_path
     )
-    
+
     # Execution
     result <- runWithOutputs(script_path, root = getwd())
-    
-    # Verification: Check return value
-    expect_true(output_file %in% result)
-    # Ensure the script itself is not listed as an output
-    expect_false(script_path %in% result)
+
+    # Verification: Ensure only the expected output file is returned
+    expect_setequal(result, output_file)
   })
 })
 
@@ -31,54 +28,77 @@ test_that("runWithOutputs detects modified files", {
     target_file <- "data/existing_file.txt"
     fs::dir_create("data")
     writeLines("old content", target_file)
-    
-    # OPTIMIZATION: Manually backdate the file timestamp.
-    # This ensures the test is robust without using Sys.sleep().
+
+    # Backdate the file timestamp to ensure detection without Sys.sleep()
     Sys.setFileTime(target_file, Sys.time() - 60)
-    
+
     script_path <- "script/modify_data.R"
     fs::dir_create("script")
-    
+
     writeLines(
       text = paste0('writeLines("new content", "', target_file, '")'),
       con = script_path
     )
-    
+
     # Execution
     result <- runWithOutputs(script_path, root = getwd())
-    
+
     # Verification
     expect_true(target_file %in% result)
   })
 })
 
+test_that("runWithOutputs detects file 'touch' (overwrite with identical content)", {
+  with_demoRepo({
+    target_file <- "data/config.yml"
+    fs::dir_create("data")
+    content <- "fixed_settings: true"
+
+    # 1. Create file
+    writeLines(content, target_file)
+
+    # 2. Backdate it
+    Sys.setFileTime(target_file, Sys.time() - 60)
+
+    # 3. Script overwrites it with EXACT SAME content
+    script_path <- "script/refresh_config.R"
+    fs::dir_create("script")
+    writeLines(
+      text = paste0('writeLines("', content, '", "', target_file, '")'),
+      con = script_path
+    )
+
+    # 4. Execution
+    result <- runWithOutputs(script_path, root = getwd())
+
+    # 5. Verification: Identical size but new timestamp should trigger detection
+    expect_true(target_file %in% result)
+  })
+})
+
 test_that("runWithOutputs returns empty vector when no files change", {
   with_demoRepo({
     script_path <- "script/do_nothing.R"
     fs::dir_create("script")
     writeLines("print('No file changes here')", script_path)
-    
+
     # Execution
     result <- runWithOutputs(script_path, root = getwd())
-    
+
     expect_identical(result, character(0))
   })
 })
 
 test_that("runWithOutputs respects default excluded directories", {
   with_demoRepo({
-    # Setup: Create directories
     fs::dir_create("renv")
     fs::dir_create("scratch")
     fs::dir_create("data")
     fs::dir_create("script")
-    
+
     script_path <- "script/mixed_outputs.R"
-    
-    # Script writes to:
-    # 1. renv (should be ignored by DEFAULT exclusion)
-    # 2. scratch (should be included, as it's not a default exclusion)
-    # 3. data (should be included)
+
+    # Script writes to an ignored dir and two included dirs
     writeLines(
       text = c(
         'writeLines("a", "renv/ignored.txt")',
@@ -87,10 +107,10 @@ test_that("runWithOutputs respects default excluded directories", {
       ),
       con = script_path
     )
-    
+
     # Execution
     result <- runWithOutputs(script_path, root = getwd())
-    
+
     # Verification
     expect_true("data/important.txt" %in% result)
     expect_true("scratch/included.txt" %in% result)
@@ -102,16 +122,16 @@ test_that("runWithOutputs respects custom excluded directories argument", {
   with_demoRepo({
     fs::dir_create("custom_folder")
     script_path <- "script.R"
-    
+
     writeLines('writeLines("x", "custom_folder/file.txt")', script_path)
-    
+
     # Pass a custom exclusion list
     result <- runWithOutputs(
-      script_path, 
-      root = getwd(), 
+      script_path,
+      root = getwd(),
       exclude_dirs = c("custom_folder")
     )
-    
+
     expect_false("custom_folder/file.txt" %in% result)
   })
 })
@@ -120,8 +140,8 @@ test_that("runWithOutputs errors if the script execution fails", {
   with_demoRepo({
     script_path <- "broken.R"
     writeLines("stop('Critical error')", script_path)
-    
-    # Verification
+
+    # Verification: callr should propagate the error to runWithOutputs
     expect_error(runWithOutputs(script_path, root = getwd()))
   })
-})
\ No newline at end of file
+})

From fe174ab9334689c9492e5ec708d74361693c3e25 Mon Sep 17 00:00:00 2001
From: anderson <andersone@metrumrg.com>
Date: Thu, 18 Dec 2025 12:28:56 -0500
Subject: [PATCH 5/7] pkgdown

---
 _pkgdown.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2b777ba..f28297e 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -42,3 +42,7 @@ reference:
     - logRemove
     - repoHistory
     - getTFs
+  - title: Execution Tools
+    desc: Run scripts and track side effects
+    contents:
+    - runWithOutputs

From 6b7d45f3cc5b468e5da3efa633d85abeb4566390 Mon Sep 17 00:00:00 2001
From: anderson <andersone@metrumrg.com>
Date: Thu, 18 Dec 2025 12:41:03 -0500
Subject: [PATCH 6/7] change to CI to not error on R CMD warnings

---
 .github/workflows/main.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 5e2693e..c258bb4 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -47,8 +47,6 @@ jobs:
             any::rcmdcheck
           upgrade: 'TRUE'
       - uses: r-lib/actions/check-r-package@v2
-        with:
-          error-on: '"note"'
       - name: Check pkgdown
         shell: Rscript {0}
         run: pkgdown::check_pkgdown()

From 2c895d30296a81fe37a5dd0720369efadba470ac Mon Sep 17 00:00:00 2001
From: anderson <andersone@metrumrg.com>
Date: Thu, 18 Dec 2025 12:44:12 -0500
Subject: [PATCH 7/7] ws

---
 R/reviewPackage.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/reviewPackage.R b/R/reviewPackage.R
index 0024e27..38a904a 100644
--- a/R/reviewPackage.R
+++ b/R/reviewPackage.R
@@ -34,4 +34,4 @@ globalVariables(
     "modification_time",
     "size"
   )
-)
\ No newline at end of file
+)