From 21b5f8ff2d2970f58884c4b28d89fe97562484f5 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Tue, 27 Aug 2024 11:28:29 -0300
Subject: [PATCH 01/13] Add interactive dialog utility functions

---
 src/utility.sh | 37 +++++++++++++++++++++++++++++++++++--
 1 file changed, 35 insertions(+), 2 deletions(-)

diff --git a/src/utility.sh b/src/utility.sh
index 441ed38..bb2025f 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -5,11 +5,11 @@ log() {
   local message="$2"
 
   print_user_message() {
-    echo "[tori] $(date "+%H:%M:%S"): $1" 1>&2
+    printf "%b\n" "[tori] $(date "+%H:%M:%S"): $1" 1>&2
   }
 
   print_debug_message() {
-    echo "$(date "+%H:%M:%N") $1" 1>&2
+    printf "%b\n" "$(date "+%H:%M:%N") $1" 1>&2
   }
 
   if [ -z "$DEBUG" ]; then
@@ -43,6 +43,39 @@ log() {
   fi
 }
 
+confirm() {
+  local question="$1"
+  local answer=
+  read -rp "$question [y/N] " answer
+
+  if [ "$answer" == y ] || [ "$answer" == Y ]; then
+    return 0;
+  else
+    return 1;
+  fi
+}
+
+ask() {
+  local question="$1"
+  local options="$2"
+  local answer=
+  local options_count=0
+  local dialog_options=
+
+  local IFS=,
+  for option in $options; do
+    _=$((options_count+=1))
+    dialog_options="$dialog_options\n [$options_count] $option"
+  done;
+  IFS=
+
+  printf "%s" "$question" >&2
+  printf "%b" "$dialog_options" >&2
+  printf "\n%s" "Choose an option [1-$options_count] " >&2
+  read -r answer
+  echo "$answer"
+}
+
 set_opts() {
   local target="$1"
   local sign=

From 91c4f6be4c798ac5f9f5370882224aa002420d6c Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Tue, 27 Aug 2024 11:28:43 -0300
Subject: [PATCH 02/13] Scaffold file comparison structure

---
 src/check.sh           |  1 +
 src/configuration.sh   |  2 +-
 src/file/merge_base.sh | 20 ++++++++++++++++++++
 src/index.sh           |  2 ++
 4 files changed, 24 insertions(+), 1 deletion(-)
 create mode 100644 src/file/merge_base.sh

diff --git a/src/check.sh b/src/check.sh
index b0df8ff..598802a 100644
--- a/src/check.sh
+++ b/src/check.sh
@@ -6,4 +6,5 @@ check() {
   log debug "collected bkp files:\n$bkp_files"
 
   scan_packages
+  merge_base "$base_files"
 }
diff --git a/src/configuration.sh b/src/configuration.sh
index 71a3d5a..0a9faf3 100644
--- a/src/configuration.sh
+++ b/src/configuration.sh
@@ -15,7 +15,7 @@ scan_directory() {
     done
   fi
 
-  echo "$files"
+  printf "%b" "$files"
 }
 
 scan_packages() {
diff --git a/src/file/merge_base.sh b/src/file/merge_base.sh
new file mode 100644
index 0000000..42f9d0e
--- /dev/null
+++ b/src/file/merge_base.sh
@@ -0,0 +1,20 @@
+merge_base() {
+  local base_files="$1"
+  local strategy=
+
+  for file in $base_files; do
+    log debug "[merge-base] Processing $file"
+    local absolute_path="$(echo "$file" | sed 's/^base//')"
+    log debug "[merge-base] Absolute path: $absolute_path"
+    local config_path="$CONFIG_ROOT/$file"
+    log debug "[merge-base] Config path: $config_path"
+
+    if diff "$absolute_path" "$config_path" > /dev/null; then
+      log debug "[merge-base] Files match"
+    else
+      log debug "[merge-base] Files differ"
+      strategy="$(ask "Configuration and system files differ" "Overwrite system,Overwrite config,Show difference")"
+      log debug "[merge-base] Chosen strategy: $strategy"
+    fi
+  done
+}
diff --git a/src/index.sh b/src/index.sh
index f168b74..9899f9a 100644
--- a/src/index.sh
+++ b/src/index.sh
@@ -9,3 +9,5 @@
 . "$TORI_ROOT/src/package/validate_input_packages.sh"
 . "$TORI_ROOT/src/package/package_conflict_input_parser.sh"
 . "$TORI_ROOT/src/package/update_package_cache.sh"
+
+. "$TORI_ROOT/src/file/merge_base.sh"

From e0e1920b0b193abd9095aa066031c79599c434f2 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Wed, 28 Aug 2024 09:27:06 -0300
Subject: [PATCH 03/13] Improve handling some edge cases in the ask utlity

---
 src/utility.sh | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/utility.sh b/src/utility.sh
index bb2025f..4ff19c4 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -72,8 +72,15 @@ ask() {
   printf "%s" "$question" >&2
   printf "%b" "$dialog_options" >&2
   printf "\n%s" "Choose an option [1-$options_count] " >&2
-  read -r answer
-  echo "$answer"
+  read -r read_answer
+  answer="$(echo "$read_answer" | xargs)"
+
+  if [ "$answer" -gt 0 ] 2> /dev/null && [ "$answer" -le $options_count ]; then
+    echo "$answer"
+  else
+    log debug "[ask] Invalid choice"
+    return 1
+  fi
 }
 
 set_opts() {

From 1b9e519e05c853a21b658e628c028e9f9abcb833 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Fri, 30 Aug 2024 09:49:38 -0300
Subject: [PATCH 04/13] Implement tree strategy for file merging

---
 src/check.sh           |  2 +-
 src/file/file_merge.sh | 61 ++++++++++++++++++++++++++++++++++++++++++
 src/file/merge_base.sh | 20 --------------
 src/index.sh           |  2 +-
 src/utility.sh         |  4 +++
 5 files changed, 67 insertions(+), 22 deletions(-)
 create mode 100644 src/file/file_merge.sh
 delete mode 100644 src/file/merge_base.sh

diff --git a/src/check.sh b/src/check.sh
index 598802a..b3923b7 100644
--- a/src/check.sh
+++ b/src/check.sh
@@ -6,5 +6,5 @@ check() {
   log debug "collected bkp files:\n$bkp_files"
 
   scan_packages
-  merge_base "$base_files"
+  merge_files "$base_files"
 }
diff --git a/src/file/file_merge.sh b/src/file/file_merge.sh
new file mode 100644
index 0000000..7bc4d0a
--- /dev/null
+++ b/src/file/file_merge.sh
@@ -0,0 +1,61 @@
+merge_files() {
+  local base_files="$1"
+  local strategy="${2:-tree}"
+
+  if [ "$strategy" == tree ]; then
+    log info "[merge_files] Merging with $strategy strategy"
+    if ! file_scan_tree "$base_files"; then
+      file_merge_tree "$base_files"
+      log info "[merge_files] Recursing"
+      merge_files "$base_files"
+    fi
+  fi
+}
+
+file_scan_tree() {
+  local base_files="$1"
+
+  for file in $base_files; do
+    local absolute_path="$(echo "$file" | sed 's/^base//')"
+    local config_path="$CONFIG_ROOT/$file"
+
+    if ! diff "$absolute_path" "$config_path" > /dev/null; then
+      return 1
+    fi
+  done
+  return 0
+}
+
+# TODO Check if files exist before acting
+file_merge_tree() {
+  local base_files="$1"
+  local strategy=
+
+  for file in $base_files; do
+    log debug "[merge_tree] Processing $file"
+    local absolute_path="$(echo "$file" | sed 's/^base//')"
+    log debug "[merge_tree] Absolute path: $absolute_path"
+    local config_path="$CONFIG_ROOT/$file"
+    log debug "[merge_tree] Config path: $config_path"
+
+    if diff "$absolute_path" "$config_path" > /dev/null; then
+      log debug "[merge_tree] Files match"
+    else
+      log debug "[merge_tree] Files differ"
+      strategy="$(ask "Differs: $(tildify "$absolute_path")" \
+        "Overwrite system,Overwrite configuration,Show difference")"
+      log debug "[merge_tree] Chosen strategy: $strategy"
+
+      if [ "$strategy" -eq 1 ]; then
+        cp -vi "$config_path" "$absolute_path"
+      elif [ "$strategy" -eq 2 ]; then
+        cp -vi "$absolute_path" "$config_path"
+      elif [ "$strategy" -eq 3 ]; then
+        echo "< $(tildify "$absolute_path") | $(echo "$config_path" | sed "s*$CONFIG_ROOT/**") >"
+        diff "$absolute_path" "$config_path" || return 0
+      else
+        log user 'Invalid choice'
+      fi
+    fi
+  done
+}
diff --git a/src/file/merge_base.sh b/src/file/merge_base.sh
deleted file mode 100644
index 42f9d0e..0000000
--- a/src/file/merge_base.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-merge_base() {
-  local base_files="$1"
-  local strategy=
-
-  for file in $base_files; do
-    log debug "[merge-base] Processing $file"
-    local absolute_path="$(echo "$file" | sed 's/^base//')"
-    log debug "[merge-base] Absolute path: $absolute_path"
-    local config_path="$CONFIG_ROOT/$file"
-    log debug "[merge-base] Config path: $config_path"
-
-    if diff "$absolute_path" "$config_path" > /dev/null; then
-      log debug "[merge-base] Files match"
-    else
-      log debug "[merge-base] Files differ"
-      strategy="$(ask "Configuration and system files differ" "Overwrite system,Overwrite config,Show difference")"
-      log debug "[merge-base] Chosen strategy: $strategy"
-    fi
-  done
-}
diff --git a/src/index.sh b/src/index.sh
index 9899f9a..95c9f91 100644
--- a/src/index.sh
+++ b/src/index.sh
@@ -10,4 +10,4 @@
 . "$TORI_ROOT/src/package/package_conflict_input_parser.sh"
 . "$TORI_ROOT/src/package/update_package_cache.sh"
 
-. "$TORI_ROOT/src/file/merge_base.sh"
+. "$TORI_ROOT/src/file/file_merge.sh"
diff --git a/src/utility.sh b/src/utility.sh
index 4ff19c4..f713db0 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -83,6 +83,10 @@ ask() {
   fi
 }
 
+tildify() {
+  echo "$1" | sed "s*$HOME*~*"
+}
+
 set_opts() {
   local target="$1"
   local sign=

From 85151e1de6f0f36bd31045fb9e21ac6bfeb6bf65 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Sat, 31 Aug 2024 07:56:35 -0300
Subject: [PATCH 05/13] Handle file not exiting when merging files

---
 src/file/file_merge.sh | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/src/file/file_merge.sh b/src/file/file_merge.sh
index 7bc4d0a..97075d7 100644
--- a/src/file/file_merge.sh
+++ b/src/file/file_merge.sh
@@ -5,9 +5,9 @@ merge_files() {
   if [ "$strategy" == tree ]; then
     log info "[merge_files] Merging with $strategy strategy"
     if ! file_scan_tree "$base_files"; then
-      file_merge_tree "$base_files"
-      log info "[merge_files] Recursing"
-      merge_files "$base_files"
+      if ! file_merge_tree "$base_files"; then
+        merge_files "$base_files"
+      fi
     fi
   fi
 }
@@ -19,14 +19,13 @@ file_scan_tree() {
     local absolute_path="$(echo "$file" | sed 's/^base//')"
     local config_path="$CONFIG_ROOT/$file"
 
-    if ! diff "$absolute_path" "$config_path" > /dev/null; then
+    if ! diff "$absolute_path" "$config_path" > /dev/null 2>&1; then
       return 1
     fi
   done
   return 0
 }
 
-# TODO Check if files exist before acting
 file_merge_tree() {
   local base_files="$1"
   local strategy=
@@ -38,21 +37,32 @@ file_merge_tree() {
     local config_path="$CONFIG_ROOT/$file"
     log debug "[merge_tree] Config path: $config_path"
 
-    if diff "$absolute_path" "$config_path" > /dev/null; then
+    if diff "$absolute_path" "$config_path" > /dev/null 2>&1; then
       log debug "[merge_tree] Files match"
     else
       log debug "[merge_tree] Files differ"
-      strategy="$(ask "Differs: $(tildify "$absolute_path")" \
-        "Overwrite system,Overwrite configuration,Show difference")"
+      local prompt_verb="Differs"
+        local prompt_options="Overwrite system,Overwrite configuration,Show difference"
+      if ! [ -f "$absolute_path" ]; then
+        local prompt_verb="In configuration only"
+        local prompt_options="Copy to system"
+      fi
+      strategy="$(ask "$prompt_verb: $(tildify "$absolute_path")" "$prompt_options")" ||
+        file_merge_tree "$base_files"
       log debug "[merge_tree] Chosen strategy: $strategy"
 
-      if [ "$strategy" -eq 1 ]; then
+      if [ "$strategy" -eq 0 ]; then
+        return 0
+      elif [ "$strategy" -eq 1 ]; then
         cp -vi "$config_path" "$absolute_path"
+        return 1
       elif [ "$strategy" -eq 2 ]; then
         cp -vi "$absolute_path" "$config_path"
+        return 1
       elif [ "$strategy" -eq 3 ]; then
         echo "< $(tildify "$absolute_path") | $(echo "$config_path" | sed "s*$CONFIG_ROOT/**") >"
-        diff "$absolute_path" "$config_path" || return 0
+        diff "$absolute_path" "$config_path"
+        return 1
       else
         log user 'Invalid choice'
       fi

From a0fdbe014937adce0dad19b99a278723afe6455c Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Sat, 31 Aug 2024 07:56:41 -0300
Subject: [PATCH 06/13] Add an exit option to ask dialog

---
 src/utility.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/utility.sh b/src/utility.sh
index f713db0..79afd4d 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -68,14 +68,15 @@ ask() {
     dialog_options="$dialog_options\n [$options_count] $option"
   done;
   IFS=
+  dialog_options="$dialog_options\n [0] Exit"
 
   printf "%s" "$question" >&2
   printf "%b" "$dialog_options" >&2
-  printf "\n%s" "Choose an option [1-$options_count] " >&2
+  printf "\n%s" "Choose an option number: " >&2
   read -r read_answer
   answer="$(echo "$read_answer" | xargs)"
 
-  if [ "$answer" -gt 0 ] 2> /dev/null && [ "$answer" -le $options_count ]; then
+  if [ "$answer" -ge 0 ] 2> /dev/null && [ "$answer" -le $options_count ]; then
     echo "$answer"
   else
     log debug "[ask] Invalid choice"

From 005638bef42cd5d11e25467762e8619f6066c9b3 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Sun, 1 Sep 2024 22:22:34 -0300
Subject: [PATCH 07/13] Improve edge cases for handling empty inputs

---
 src/file/file_merge.sh | 4 ++--
 src/utility.sh         | 9 +++++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/file/file_merge.sh b/src/file/file_merge.sh
index 97075d7..7bf25dc 100644
--- a/src/file/file_merge.sh
+++ b/src/file/file_merge.sh
@@ -47,8 +47,7 @@ file_merge_tree() {
         local prompt_verb="In configuration only"
         local prompt_options="Copy to system"
       fi
-      strategy="$(ask "$prompt_verb: $(tildify "$absolute_path")" "$prompt_options")" ||
-        file_merge_tree "$base_files"
+      strategy="$(ask "$prompt_verb: $(tildify "$absolute_path")" "$prompt_options")"
       log debug "[merge_tree] Chosen strategy: $strategy"
 
       if [ "$strategy" -eq 0 ]; then
@@ -65,6 +64,7 @@ file_merge_tree() {
         return 1
       else
         log user 'Invalid choice'
+        return 1
       fi
     fi
   done
diff --git a/src/utility.sh b/src/utility.sh
index 79afd4d..b342897 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -76,10 +76,15 @@ ask() {
   read -r read_answer
   answer="$(echo "$read_answer" | xargs)"
 
-  if [ "$answer" -ge 0 ] 2> /dev/null && [ "$answer" -le $options_count ]; then
+  if [ -z "$answer" ]; then
+    log info "[ask] Invalid choice"
+    echo -1
+    return 1
+  elif [ "$answer" -ge 0 ] 2> /dev/null && [ "$answer" -le $options_count ]; then
     echo "$answer"
   else
-    log debug "[ask] Invalid choice"
+    log info "[ask] Invalid choice"
+    echo -1
     return 1
   fi
 }

From 7b2f1494b944b89660122f78bd18a183e2a46094 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Sun, 1 Sep 2024 22:23:28 -0300
Subject: [PATCH 08/13] Refactor directory variable names for uniformity

---
 src/package/package_conflict_input_parser.sh |  4 ++--
 src/package/package_conflict_resolution.sh   |  8 ++++----
 src/utility.sh                               | 12 ++++++++----
 tori                                         |  7 ++++---
 4 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/src/package/package_conflict_input_parser.sh b/src/package/package_conflict_input_parser.sh
index 6c5d9e7..547db98 100644
--- a/src/package/package_conflict_input_parser.sh
+++ b/src/package/package_conflict_input_parser.sh
@@ -1,8 +1,8 @@
 package_conflict_input_parser() {
   local packages="$1"
   local conflict_type="$2"
-  local input="$TMP_DIR/package_conflict_input"
-  local input_choices="$TMP_DIR/package_conflict_input_choices"
+  local input="$TMP_ROOT/package_conflict_input"
+  local input_choices="$TMP_ROOT/package_conflict_input_choices"
   local choices=
   local packages_to_install=
   local packages_to_uninstall=
diff --git a/src/package/package_conflict_resolution.sh b/src/package/package_conflict_resolution.sh
index f2ba8dd..e7b4efc 100644
--- a/src/package/package_conflict_resolution.sh
+++ b/src/package/package_conflict_resolution.sh
@@ -3,18 +3,18 @@ resolve_packages() {
   local input_packages=
 
   # shellcheck disable=SC2154
-  ( echo "$system_packages" > "$TMP_DIR/system_packages"
-    echo "$user_packages" > "$TMP_DIR/user_packages" )
+  ( echo "$system_packages" > "$TMP_ROOT/system_packages"
+    echo "$user_packages" > "$TMP_ROOT/user_packages" )
 
   local packages_not_on_configuration="$(grep -v -x -f \
-    "$TMP_DIR/user_packages" "$TMP_DIR/system_packages" | xargs)"
+    "$TMP_ROOT/user_packages" "$TMP_ROOT/system_packages" | xargs)"
 
   if [ -n "$packages_not_on_configuration" ]; then
     not_on_configuration_dialog "$packages_not_on_configuration"
   fi
 
   local packages_not_installed=$(grep -v -x -f \
-    "$TMP_DIR/system_packages" "$TMP_DIR/user_packages" | xargs)
+    "$TMP_ROOT/system_packages" "$TMP_ROOT/user_packages" | xargs)
 
   if [ -n "$packages_not_installed" ]; then
     not_installed_dialog "$packages_not_installed"
diff --git a/src/utility.sh b/src/utility.sh
index b342897..82a8e91 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -124,12 +124,16 @@ set_opts() {
 }
 
 prepare_directories() {
-  if ! [ -d "$TMP_DIR" ]; then
-    mkdir "$TMP_DIR"
+  if ! [ -d "$TMP_ROOT" ]; then
+    mkdir "$TMP_ROOT"
   fi
 
-  if ! [ -d "$CACHE_DIR" ]; then
-    mkdir -p "$CACHE_DIR"
+  if ! [ -d "$CACHE_ROOT" ]; then
+    mkdir -p "$CACHE_ROOT"
+  fi
+
+  if ! [ -d "$BACKUP_ROOT" ]; then
+    mkdir -p "$BACKUP_ROOT"
   fi
 
   if ! [ -d "$CONFIG_ROOT" ]; then
diff --git a/tori b/tori
index 6009659..e2e92e7 100755
--- a/tori
+++ b/tori
@@ -5,8 +5,9 @@ main() {
   VERSION="0.5.0 2024-07-18"
   TORI_ROOT="$HOME/.local/share/tori"
   CONFIG_ROOT="$HOME/.config/tori"
-  TMP_DIR="/tmp/tori"
-  CACHE_DIR="$HOME/.cache/tori"
+  BACKUP_ROOT="$HOME/.local/state/tori/backup"
+  TMP_ROOT="/tmp/tori"
+  CACHE_ROOT="$HOME/.cache/tori"
 
   # os-independent state
 
@@ -25,7 +26,7 @@ main() {
 
   ## os-dependent state
   OS="$(get_operating_system)"
-  PACKAGE_CACHE="$CACHE_DIR/${OS}_packages.cache"
+  PACKAGE_CACHE="$CACHE_ROOT/${OS}_packages.cache"
 
   base_files=
   bkp_files=

From 4b6a9569954df8f6688100ca77f7e9d79764f845 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Sun, 1 Sep 2024 22:48:34 -0300
Subject: [PATCH 09/13] Implement backing up before overwriting files

---
 src/file/backup.sh     | 28 ++++++++++++++++++++++++++++
 src/file/file_merge.sh |  2 ++
 src/index.sh           |  1 +
 src/utility.sh         |  6 ++++++
 4 files changed, 37 insertions(+)
 create mode 100644 src/file/backup.sh

diff --git a/src/file/backup.sh b/src/file/backup.sh
new file mode 100644
index 0000000..7a05c2c
--- /dev/null
+++ b/src/file/backup.sh
@@ -0,0 +1,28 @@
+# takes a list of space-separated absolute paths 
+# backs each path up, creating canonical or ephemeral copies as needed
+backup_paths() {
+  local paths="$1"
+  local canonical_path=
+  local ephemeral_path=
+
+  for path in $paths; do
+    canonical_path="$BACKUP_ROOT/canonical$path"
+    timestamp="$(date +'%Y-%m-%dT%H-%M-%S')"
+    ephemeral_path="$BACKUP_ROOT/ephemeral${path}_$timestamp"
+
+    if [ -f "$canonical_path" ]; then
+      log debug "[backup] Creating ephemeral copy for $path"
+      mkdir -p "$(dirname "$ephemeral_path")"
+      if [ -f "$ephemeral_path" ]; then
+        log debug "[backup] Overwriting ephemeral copy for $path"
+        cp -f "$path" "$ephemeral_path"
+      else
+        cp "$path" "$ephemeral_path"
+      fi
+    else
+      log debug "[backup] Creating canonical copy for $path"
+      mkdir -p "$(dirname "$canonical_path")"
+      cp "$path" "$canonical_path"
+    fi
+  done
+}
diff --git a/src/file/file_merge.sh b/src/file/file_merge.sh
index 7bf25dc..46e75be 100644
--- a/src/file/file_merge.sh
+++ b/src/file/file_merge.sh
@@ -53,9 +53,11 @@ file_merge_tree() {
       if [ "$strategy" -eq 0 ]; then
         return 0
       elif [ "$strategy" -eq 1 ]; then
+        backup_paths "$absolute_path"
         cp -vi "$config_path" "$absolute_path"
         return 1
       elif [ "$strategy" -eq 2 ]; then
+        backup_paths "$config_path"
         cp -vi "$absolute_path" "$config_path"
         return 1
       elif [ "$strategy" -eq 3 ]; then
diff --git a/src/index.sh b/src/index.sh
index 95c9f91..0af2c73 100644
--- a/src/index.sh
+++ b/src/index.sh
@@ -11,3 +11,4 @@
 . "$TORI_ROOT/src/package/update_package_cache.sh"
 
 . "$TORI_ROOT/src/file/file_merge.sh"
+. "$TORI_ROOT/src/file/backup.sh"
diff --git a/src/utility.sh b/src/utility.sh
index 82a8e91..78b6de3 100644
--- a/src/utility.sh
+++ b/src/utility.sh
@@ -134,6 +134,12 @@ prepare_directories() {
 
   if ! [ -d "$BACKUP_ROOT" ]; then
     mkdir -p "$BACKUP_ROOT"
+    if ! [ -d "$BACKUP_ROOT/canonical" ]; then
+      mkdir "$BACKUP_ROOT/canonical"
+    fi
+    if ! [ -d "$BACKUP_ROOT/ephemeral" ]; then
+      mkdir "$BACKUP_ROOT/ephemeral"
+    fi
   fi
 
   if ! [ -d "$CONFIG_ROOT" ]; then

From 59e040d59789dcf75a78ff4da9e2c0ec3fdd254b Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Tue, 3 Sep 2024 08:57:55 -0300
Subject: [PATCH 10/13] Extract authorization command to top level

---
 src/package/package_manager.sh | 7 +++----
 tori                           | 4 ++--
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/package/package_manager.sh b/src/package/package_manager.sh
index f96f132..4303ce8 100644
--- a/src/package/package_manager.sh
+++ b/src/package/package_manager.sh
@@ -2,7 +2,6 @@ package_manager() {
   local command="$1"
 
   local manager
-  local authorizer="sudo"
   local args__install
   local args__uninstall
   local args__get_manually_installed
@@ -25,11 +24,11 @@ package_manager() {
   if [ "$command" = 'get_manually_installed' ]; then
     eval $manager "$args__get_manually_installed"
   elif [ "$command" = 'install' ]; then
-    $authorizer $manager $args__install $args__user_args
+    $AUTHORIZE_COMMAND $manager $args__install $args__user_args
   elif [ "$command" = 'uninstall' ]; then
-    $authorizer $manager $args__uninstall $args__user_args
+    $AUTHORIZE_COMMAND $manager $args__uninstall $args__user_args
   elif [ "$command" = 'update' ]; then
-    $authorizer $manager $args__update
+    $AUTHORIZE_COMMAND $manager $args__update
   elif [ "$command" = 'get_available' ]; then
     eval $manager "$args__get_available"
   else
diff --git a/tori b/tori
index e2e92e7..3c15354 100755
--- a/tori
+++ b/tori
@@ -19,14 +19,14 @@ main() {
   parameter="$2"
 
   # import source
-
   check_core_paths
   . "$TORI_ROOT/src/index.sh"
-  set_opts on
 
   ## os-dependent state
+  set_opts on
   OS="$(get_operating_system)"
   PACKAGE_CACHE="$CACHE_ROOT/${OS}_packages.cache"
+  AUTHORIZE_COMMAND="sudo"
 
   base_files=
   bkp_files=

From de634f3749c834b16ede0478eaa98af3dc0fdc5f Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Tue, 3 Sep 2024 09:23:37 -0300
Subject: [PATCH 11/13] Handle permissions when reading and writing files

---
 src/file/file_merge.sh | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/file/file_merge.sh b/src/file/file_merge.sh
index 46e75be..c938431 100644
--- a/src/file/file_merge.sh
+++ b/src/file/file_merge.sh
@@ -54,15 +54,27 @@ file_merge_tree() {
         return 0
       elif [ "$strategy" -eq 1 ]; then
         backup_paths "$absolute_path"
-        cp -vi "$config_path" "$absolute_path"
+        if [ -r "$config_path" ] && [ -w "$absolute_path" ]; then
+          cp -vi "$config_path" "$absolute_path"
+        else
+          $AUTHORIZE_COMMAND cp -vi "$config_path" "$absolute_path"
+        fi
         return 1
       elif [ "$strategy" -eq 2 ]; then
         backup_paths "$config_path"
-        cp -vi "$absolute_path" "$config_path"
+        if [ -r "$absolute_path" ] && [ -w "$config_path" ]; then
+          cp -vi "$absolute_path" "$config_path"
+        else
+          $AUTHORIZE_COMMAND cp -vi "$absolute_path" "$config_path"
+        fi
         return 1
       elif [ "$strategy" -eq 3 ]; then
         echo "< $(tildify "$absolute_path") | $(echo "$config_path" | sed "s*$CONFIG_ROOT/**") >"
-        diff "$absolute_path" "$config_path"
+        if [ -r "$absolute_path" ] && [ -r "$config_path" ]; then
+          diff "$absolute_path" "$config_path"
+        else
+          $AUTHORIZE_COMMAND diff "$absolute_path" "$config_path"
+        fi
         return 1
       else
         log user 'Invalid choice'

From e94e68540f7395359b0ede4f21f5b6b4769828ab Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Tue, 3 Sep 2024 12:09:40 -0300
Subject: [PATCH 12/13] Make file operations more permission-aware

---
 src/file/backup.sh     | 20 ++++++++++++++++----
 src/file/file_merge.sh | 14 +++++++-------
 2 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/src/file/backup.sh b/src/file/backup.sh
index 7a05c2c..7f992a7 100644
--- a/src/file/backup.sh
+++ b/src/file/backup.sh
@@ -1,4 +1,4 @@
-# takes a list of space-separated absolute paths 
+# takes a list of newline-separated absolute paths 
 # backs each path up, creating canonical or ephemeral copies as needed
 backup_paths() {
   local paths="$1"
@@ -15,14 +15,26 @@ backup_paths() {
       mkdir -p "$(dirname "$ephemeral_path")"
       if [ -f "$ephemeral_path" ]; then
         log debug "[backup] Overwriting ephemeral copy for $path"
-        cp -f "$path" "$ephemeral_path"
+        if [ -r "$path" ]; then
+          cp -f "$path" "$ephemeral_path"
+        else
+          $AUTHORIZE_COMMAND cp -f "$path" "$ephemeral_path"
+        fi
       else
-        cp "$path" "$ephemeral_path"
+        if [ -r "$path" ]; then
+          cp "$path" "$ephemeral_path"
+        else
+          $AUTHORIZE_COMMAND cp "$path" "$ephemeral_path"
+        fi
       fi
     else
       log debug "[backup] Creating canonical copy for $path"
       mkdir -p "$(dirname "$canonical_path")"
-      cp "$path" "$canonical_path"
+      if [ -r "$path" ]; then
+        cp "$path" "$canonical_path"
+      else
+        $AUTHORIZE_COMMAND cp "$path" "$canonical_path"
+      fi
     fi
   done
 }
diff --git a/src/file/file_merge.sh b/src/file/file_merge.sh
index c938431..ffd61f4 100644
--- a/src/file/file_merge.sh
+++ b/src/file/file_merge.sh
@@ -28,7 +28,7 @@ file_scan_tree() {
 
 file_merge_tree() {
   local base_files="$1"
-  local strategy=
+  local overwrite_choice=
 
   for file in $base_files; do
     log debug "[merge_tree] Processing $file"
@@ -47,12 +47,12 @@ file_merge_tree() {
         local prompt_verb="In configuration only"
         local prompt_options="Copy to system"
       fi
-      strategy="$(ask "$prompt_verb: $(tildify "$absolute_path")" "$prompt_options")"
-      log debug "[merge_tree] Chosen strategy: $strategy"
+      overwrite_choice="$(ask "$prompt_verb: $(tildify "$absolute_path")" "$prompt_options")"
+      log debug "[merge_tree] Overwrite choice: $overwrite_choice"
 
-      if [ "$strategy" -eq 0 ]; then
+      if [ "$overwrite_choice" -eq 0 ]; then
         return 0
-      elif [ "$strategy" -eq 1 ]; then
+      elif [ "$overwrite_choice" -eq 1 ]; then
         backup_paths "$absolute_path"
         if [ -r "$config_path" ] && [ -w "$absolute_path" ]; then
           cp -vi "$config_path" "$absolute_path"
@@ -60,7 +60,7 @@ file_merge_tree() {
           $AUTHORIZE_COMMAND cp -vi "$config_path" "$absolute_path"
         fi
         return 1
-      elif [ "$strategy" -eq 2 ]; then
+      elif [ "$overwrite_choice" -eq 2 ]; then
         backup_paths "$config_path"
         if [ -r "$absolute_path" ] && [ -w "$config_path" ]; then
           cp -vi "$absolute_path" "$config_path"
@@ -68,7 +68,7 @@ file_merge_tree() {
           $AUTHORIZE_COMMAND cp -vi "$absolute_path" "$config_path"
         fi
         return 1
-      elif [ "$strategy" -eq 3 ]; then
+      elif [ "$overwrite_choice" -eq 3 ]; then
         echo "< $(tildify "$absolute_path") | $(echo "$config_path" | sed "s*$CONFIG_ROOT/**") >"
         if [ -r "$absolute_path" ] && [ -r "$config_path" ]; then
           diff "$absolute_path" "$config_path"

From 67de45f5ba53e7fb61902e96c6fd4ea4a4c52579 Mon Sep 17 00:00:00 2001
From: jutty <j@jutty.dev>
Date: Tue, 3 Sep 2024 12:09:51 -0300
Subject: [PATCH 13/13] Update strings for v0.6.0

---
 CHANGELOG | 4 ++++
 README.md | 2 +-
 tori      | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index 759fd6f..92c1843 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+0.6.0 2024-09-03: File management with the tree strategy
+									File backups
+                  Extract authorization command to top level
+                  ask and tildify utility functions
 0.5.0 2024-07-18: "Decide in editor" package conflict resolution strategy
                   Drop pipefail shell option for dash compatibility
                   Add numerical debug levels to the log utility function
diff --git a/README.md b/README.md
index c25a9a3..138a64c 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 tori is a tool to track your personal systems' configurations and replicate them.
 
-If you'd like a more detailed description of what it is, its purpose, origins and goals, see the [announcement blog post](https://blog.jutty.dev/posts/introducing-tori.html).
+If you'd like a more detailed description of what it is, its purpose, origins and goals, see the [announcement blog post](https://blog.jutty.dev/posts/introducing-tori/).
 
 Refer to the [project website](https://tori.jutty.dev) for updates and access to [documentation](https://tori.jutty.dev/docs).
 
diff --git a/tori b/tori
index 3c15354..2d0e2b5 100755
--- a/tori
+++ b/tori
@@ -2,7 +2,7 @@
 
 main() {
   # paths
-  VERSION="0.5.0 2024-07-18"
+  VERSION="0.6.0 2024-09-03"
   TORI_ROOT="$HOME/.local/share/tori"
   CONFIG_ROOT="$HOME/.config/tori"
   BACKUP_ROOT="$HOME/.local/state/tori/backup"