diff --git a/scripts/easy-docker/lib/app/wizard/common/apps/metadata.sh b/scripts/easy-docker/lib/app/wizard/common/apps/metadata.sh
index 9dbbb498..3dba35b4 100755
--- a/scripts/easy-docker/lib/app/wizard/common/apps/metadata.sh
+++ b/scripts/easy-docker/lib/app/wizard/common/apps/metadata.sh
@@ -253,126 +253,3 @@ persist_stack_apps_json_from_metadata_apps() {
 
   return 0
 }
-
-persist_stack_metadata_top_level_object() {
-  local stack_dir="${1}"
-  local object_key="${2}"
-  local object_json="${3}"
-  local insert_before_key="${4:-}"
-  local metadata_path=""
-  local metadata_tmp_path=""
-
-  metadata_path="${stack_dir}/metadata.json"
-  metadata_tmp_path="${metadata_path}.tmp"
-  if [ ! -f "${metadata_path}" ]; then
-    return 1
-  fi
-
-  if [ -z "${object_json}" ]; then
-    return 1
-  fi
-
-  if ! awk -v object_key="${object_key}" -v object_json="${object_json}" -v insert_before_key="${insert_before_key}" '
-    BEGIN {
-      target_regex = "^  \"" object_key "\"[[:space:]]*:"
-      before_regex = ""
-      if (insert_before_key != "") {
-        before_regex = "^  \"" insert_before_key "\"[[:space:]]*:"
-      }
-      in_target = 0
-      target_depth = 0
-      inserted = 0
-      prev = ""
-    }
-    function flush_prev() {
-      if (prev != "") {
-        print prev
-        prev = ""
-      }
-    }
-    {
-      if (!in_target && $0 ~ target_regex) {
-        flush_prev()
-        if (object_key == "wizard") {
-          print "  \"" object_key "\": " object_json
-        } else {
-          print "  \"" object_key "\": " object_json ","
-        }
-        in_target = 1
-        inserted = 1
-        if ($0 ~ /{/) {
-          target_depth += gsub(/{/, "{", $0)
-          target_depth -= gsub(/}/, "}", $0)
-        } else {
-          target_depth = 0
-        }
-        if (target_depth <= 0) {
-          in_target = 0
-        }
-        next
-      }
-
-      if (in_target) {
-        target_depth += gsub(/{/, "{", $0)
-        target_depth -= gsub(/}/, "}", $0)
-        if (target_depth <= 0) {
-          in_target = 0
-        }
-        next
-      }
-
-      if (!inserted && before_regex != "" && $0 ~ before_regex) {
-        flush_prev()
-        print "  \"" object_key "\": " object_json ","
-        inserted = 1
-      }
-
-      if (!inserted && $0 ~ /^}/) {
-        if (prev != "") {
-          if (prev !~ /,[[:space:]]*$/) {
-            prev = prev ","
-          }
-          print prev
-          prev = ""
-        }
-        print "  \"" object_key "\": " object_json
-        inserted = 1
-        print $0
-        next
-      }
-
-      flush_prev()
-      prev = $0
-    }
-    END {
-      flush_prev()
-      if (!inserted) {
-        exit 2
-      }
-    }
-  ' "${metadata_path}" >"${metadata_tmp_path}"; then
-    rm -f -- "${metadata_tmp_path}" >/dev/null 2>&1 || true
-    return 1
-  fi
-
-  if ! mv -- "${metadata_tmp_path}" "${metadata_path}"; then
-    rm -f -- "${metadata_tmp_path}" >/dev/null 2>&1 || true
-    return 1
-  fi
-
-  return 0
-}
-
-persist_stack_metadata_apps_object() {
-  local stack_dir="${1}"
-  local apps_json_object="${2}"
-
-  persist_stack_metadata_top_level_object "${stack_dir}" "apps" "${apps_json_object}" "wizard"
-}
-
-persist_stack_metadata_wizard_object() {
-  local stack_dir="${1}"
-  local wizard_json_object="${2}"
-
-  persist_stack_metadata_top_level_object "${stack_dir}" "wizard" "${wizard_json_object}"
-}
diff --git a/scripts/easy-docker/lib/app/wizard/common/apps/persistence.sh b/scripts/easy-docker/lib/app/wizard/common/apps/persistence.sh
index e581f3cc..4a1dead2 100755
--- a/scripts/easy-docker/lib/app/wizard/common/apps/persistence.sh
+++ b/scripts/easy-docker/lib/app/wizard/common/apps/persistence.sh
@@ -1,8 +1,10 @@
 #!/usr/bin/env bash
 
-persist_stack_metadata_apps_object() {
+persist_stack_metadata_top_level_object() {
   local stack_dir="${1}"
-  local apps_json_object="${2}"
+  local object_key="${2}"
+  local object_json="${3}"
+  local insert_before_key="${4:-}"
   local metadata_path=""
   local metadata_tmp_path=""
 
@@ -12,14 +14,19 @@ persist_stack_metadata_apps_object() {
     return 1
   fi
 
-  if [ -z "${apps_json_object}" ]; then
+  if [ -z "${object_json}" ]; then
     return 1
   fi
 
-  if ! awk -v apps_object="${apps_json_object}" '
+  if ! awk -v object_key="${object_key}" -v object_json="${object_json}" -v insert_before_key="${insert_before_key}" '
     BEGIN {
-      in_top_level_apps = 0
-      apps_depth = 0
+      target_regex = "^  \"" object_key "\"[[:space:]]*:"
+      before_regex = ""
+      if (insert_before_key != "") {
+        before_regex = "^  \"" insert_before_key "\"[[:space:]]*:"
+      }
+      in_target = 0
+      target_depth = 0
       inserted = 0
       prev = ""
     }
@@ -30,35 +37,39 @@ persist_stack_metadata_apps_object() {
       }
     }
     {
-      if (!in_top_level_apps && $0 ~ /^  "apps"[[:space:]]*:/) {
+      if (!in_target && $0 ~ target_regex) {
         flush_prev()
-        print "  \"apps\": " apps_object ","
-        in_top_level_apps = 1
+        if (object_key == "wizard") {
+          print "  \"" object_key "\": " object_json
+        } else {
+          print "  \"" object_key "\": " object_json ","
+        }
+        in_target = 1
         inserted = 1
         if ($0 ~ /{/) {
-          apps_depth += gsub(/{/, "{", $0)
-          apps_depth -= gsub(/}/, "}", $0)
+          target_depth += gsub(/{/, "{", $0)
+          target_depth -= gsub(/}/, "}", $0)
         } else {
-          apps_depth = 0
+          target_depth = 0
         }
-        if (apps_depth <= 0) {
-          in_top_level_apps = 0
+        if (target_depth <= 0) {
+          in_target = 0
         }
         next
       }
 
-      if (in_top_level_apps) {
-        apps_depth += gsub(/{/, "{", $0)
-        apps_depth -= gsub(/}/, "}", $0)
-        if (apps_depth <= 0) {
-          in_top_level_apps = 0
+      if (in_target) {
+        target_depth += gsub(/{/, "{", $0)
+        target_depth -= gsub(/}/, "}", $0)
+        if (target_depth <= 0) {
+          in_target = 0
         }
         next
       }
 
-      if (!inserted && $0 ~ /^  "wizard"[[:space:]]*:/) {
+      if (!inserted && before_regex != "" && $0 ~ before_regex) {
         flush_prev()
-        print "  \"apps\": " apps_object ","
+        print "  \"" object_key "\": " object_json ","
         inserted = 1
       }
 
@@ -70,7 +81,7 @@ persist_stack_metadata_apps_object() {
           print prev
           prev = ""
         }
-        print "  \"apps\": " apps_object
+        print "  \"" object_key "\": " object_json
         inserted = 1
         print $0
         next
@@ -98,94 +109,16 @@ persist_stack_metadata_apps_object() {
   return 0
 }
 
+persist_stack_metadata_apps_object() {
+  local stack_dir="${1}"
+  local apps_json_object="${2}"
+
+  persist_stack_metadata_top_level_object "${stack_dir}" "apps" "${apps_json_object}" "wizard"
+}
+
 persist_stack_metadata_wizard_object() {
   local stack_dir="${1}"
   local wizard_json_object="${2}"
-  local metadata_path=""
-  local metadata_tmp_path=""
 
-  metadata_path="${stack_dir}/metadata.json"
-  metadata_tmp_path="${metadata_path}.tmp"
-  if [ ! -f "${metadata_path}" ]; then
-    return 1
-  fi
-
-  if [ -z "${wizard_json_object}" ]; then
-    return 1
-  fi
-
-  if ! awk -v wizard_object="${wizard_json_object}" '
-    BEGIN {
-      in_top_level_wizard = 0
-      wizard_depth = 0
-      inserted = 0
-      prev = ""
-    }
-    function flush_prev() {
-      if (prev != "") {
-        print prev
-        prev = ""
-      }
-    }
-    {
-      if (!in_top_level_wizard && $0 ~ /^  "wizard"[[:space:]]*:/) {
-        flush_prev()
-        print "  \"wizard\": " wizard_object
-        in_top_level_wizard = 1
-        inserted = 1
-        if ($0 ~ /{/) {
-          wizard_depth += gsub(/{/, "{", $0)
-          wizard_depth -= gsub(/}/, "}", $0)
-        } else {
-          wizard_depth = 0
-        }
-        if (wizard_depth <= 0) {
-          in_top_level_wizard = 0
-        }
-        next
-      }
-
-      if (in_top_level_wizard) {
-        wizard_depth += gsub(/{/, "{", $0)
-        wizard_depth -= gsub(/}/, "}", $0)
-        if (wizard_depth <= 0) {
-          in_top_level_wizard = 0
-        }
-        next
-      }
-
-      if (!inserted && $0 ~ /^}/) {
-        if (prev != "") {
-          if (prev !~ /,[[:space:]]*$/) {
-            prev = prev ","
-          }
-          print prev
-          prev = ""
-        }
-        print "  \"wizard\": " wizard_object
-        inserted = 1
-        print $0
-        next
-      }
-
-      flush_prev()
-      prev = $0
-    }
-    END {
-      flush_prev()
-      if (!inserted) {
-        exit 2
-      }
-    }
-  ' "${metadata_path}" >"${metadata_tmp_path}"; then
-    rm -f -- "${metadata_tmp_path}" >/dev/null 2>&1 || true
-    return 1
-  fi
-
-  if ! mv -- "${metadata_tmp_path}" "${metadata_path}"; then
-    rm -f -- "${metadata_tmp_path}" >/dev/null 2>&1 || true
-    return 1
-  fi
-
-  return 0
+  persist_stack_metadata_top_level_object "${stack_dir}" "wizard" "${wizard_json_object}"
 }
diff --git a/scripts/easy-docker/lib/app/wizard/env/apps.sh b/scripts/easy-docker/lib/app/wizard/env/apps.sh
index ea357578..4a0bbf47 100755
--- a/scripts/easy-docker/lib/app/wizard/env/apps.sh
+++ b/scripts/easy-docker/lib/app/wizard/env/apps.sh
@@ -84,12 +84,17 @@ build_predefined_apps_metadata_json_object() {
   local result_var="${1}"
   local predefined_csv="${2}"
   local branch_lines="${3}"
+  local custom_apps_lines="${4:-}"
   local app_id=""
   local app_branch=""
+  local custom_repo=""
+  local custom_branch=""
   local predefined_json_entries=""
   local branch_json_entries=""
+  local custom_json_entries=""
   local escaped_app_id=""
   local escaped_branch=""
+  local escaped_repo=""
   local entry_json=""
   local line=""
   local -a predefined_ids=()
@@ -134,7 +139,30 @@ build_predefined_apps_metadata_json_object() {
 ${branch_lines}
 EOF
 
-  printf -v "${result_var}" '{\n      "predefined": [\n%s\n      ],\n      "predefined_branches": {\n%s\n      },\n      "custom": [\n      ]\n    }' "${predefined_json_entries}" "${branch_json_entries}"
+  while IFS= read -r line; do
+    if [ -z "${line}" ]; then
+      continue
+    fi
+
+    custom_repo="${line%%|*}"
+    custom_branch="${line#*|}"
+    if [ -z "${custom_repo}" ] || [ -z "${custom_branch}" ]; then
+      continue
+    fi
+
+    escaped_repo="$(json_escape_string "${custom_repo}")"
+    escaped_branch="$(json_escape_string "${custom_branch}")"
+    entry_json="$(printf '        {\n          "repo": "%s",\n          "branch": "%s"\n        }' "${escaped_repo}" "${escaped_branch}")"
+    if [ -z "${custom_json_entries}" ]; then
+      custom_json_entries="${entry_json}"
+    else
+      custom_json_entries="${custom_json_entries}"$',\n'"${entry_json}"
+    fi
+  done <<EOF
+${custom_apps_lines}
+EOF
+
+  printf -v "${result_var}" '{\n      "predefined": [\n%s\n      ],\n      "predefined_branches": {\n%s\n      },\n      "custom": [\n%s\n      ]\n    }' "${predefined_json_entries}" "${branch_json_entries}" "${custom_json_entries}"
 }
 
 get_predefined_branch_from_lines() {
@@ -247,6 +275,7 @@ prompt_custom_modular_apps_data() {
   local preferred_branch=""
   local available_branch_lines=""
   local existing_branch_lines=""
+  local existing_custom_lines=""
   local selected_branch_lines=""
   local selected_app_count=0
   local assembled_apps_metadata_json_object=""
@@ -257,6 +286,7 @@ prompt_custom_modular_apps_data() {
   if [ -f "${metadata_path}" ]; then
     selected_predefined_csv="$(get_metadata_apps_predefined_csv "${metadata_path}" || true)"
     existing_branch_lines="$(get_metadata_apps_predefined_branch_lines "${metadata_path}" || true)"
+    existing_custom_lines="$(get_metadata_apps_custom_lines "${metadata_path}" || true)"
   fi
 
   while true; do
@@ -393,7 +423,7 @@ EOF
       continue
     fi
 
-    build_predefined_apps_metadata_json_object assembled_apps_metadata_json_object "${selected_predefined_csv}" "${selected_branch_lines}"
+    build_predefined_apps_metadata_json_object assembled_apps_metadata_json_object "${selected_predefined_csv}" "${selected_branch_lines}" "${existing_custom_lines}"
     printf -v "${result_apps_metadata_var}" "%s" "${assembled_apps_metadata_json_object}"
     return 0
   done
@@ -444,6 +474,7 @@ prompt_selected_stack_app_branches_data() {
   local preferred_branch=""
   local available_branch_lines=""
   local existing_branch_lines=""
+  local existing_custom_lines=""
   local selected_branch_lines=""
   local selected_app_count=0
   local assembled_apps_metadata_json_object=""
@@ -457,6 +488,7 @@ prompt_selected_stack_app_branches_data() {
 
   selected_predefined_csv="$(get_metadata_apps_predefined_csv "${metadata_path}" || true)"
   existing_branch_lines="$(get_metadata_apps_predefined_branch_lines "${metadata_path}" || true)"
+  existing_custom_lines="$(get_metadata_apps_custom_lines "${metadata_path}" || true)"
   if [ -z "${selected_predefined_csv}" ]; then
     return 4
   fi
@@ -515,7 +547,7 @@ prompt_selected_stack_app_branches_data() {
     return 4
   fi
 
-  build_predefined_apps_metadata_json_object assembled_apps_metadata_json_object "${selected_predefined_csv}" "${selected_branch_lines}"
+  build_predefined_apps_metadata_json_object assembled_apps_metadata_json_object "${selected_predefined_csv}" "${selected_branch_lines}" "${existing_custom_lines}"
   printf -v "${result_apps_metadata_var}" "%s" "${assembled_apps_metadata_json_object}"
   return 0
 }
diff --git a/scripts/easy-docker/lib/app/wizard/flows/manage.sh b/scripts/easy-docker/lib/app/wizard/flows/manage.sh
index 1e9a98ec..ee9fa90b 100755
--- a/scripts/easy-docker/lib/app/wizard/flows/manage.sh
+++ b/scripts/easy-docker/lib/app/wizard/flows/manage.sh
@@ -4,8 +4,8 @@ load_easy_docker_manage_flow_modules() {
   local manage_dir=""
   manage_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/manage"
 
-  # shellcheck source=scripts/easy-docker/lib/app/wizard/flows/manage/docker.sh
-  source "${manage_dir}/docker.sh"
+  # shellcheck source=scripts/easy-docker/lib/app/wizard/flows/manage/build.sh
+  source "${manage_dir}/build.sh"
   # shellcheck source=scripts/easy-docker/lib/app/wizard/flows/manage/prompts.sh
   source "${manage_dir}/prompts.sh"
   # shellcheck source=scripts/easy-docker/lib/app/wizard/flows/manage/site.sh
diff --git a/scripts/easy-docker/lib/app/wizard/flows/manage/build.sh b/scripts/easy-docker/lib/app/wizard/flows/manage/build.sh
index b6b5a4b1..6ef17921 100755
--- a/scripts/easy-docker/lib/app/wizard/flows/manage/build.sh
+++ b/scripts/easy-docker/lib/app/wizard/flows/manage/build.sh
@@ -1,5 +1,21 @@
 #!/usr/bin/env bash
 
+refresh_stack_generated_compose_with_feedback() {
+  local stack_dir="${1}"
+  local generated_compose_path=""
+  local render_compose_status=0
+
+  generated_compose_path="$(get_stack_generated_compose_path "${stack_dir}")"
+  if render_stack_compose_from_metadata "${stack_dir}"; then
+    show_warning_and_wait "Generated compose refreshed successfully: ${generated_compose_path}" 3
+    return 0
+  fi
+
+  render_compose_status=$?
+  show_warning_and_wait "The image build succeeded, but generated compose could not be refreshed (${render_compose_status}) for ${generated_compose_path}." 4
+  return "${render_compose_status}"
+}
+
 run_build_stack_custom_image_with_feedback() {
   local stack_name="${1}"
   local stack_dir="${2}"
@@ -8,6 +24,7 @@ run_build_stack_custom_image_with_feedback() {
   show_warning_message "Starting docker build for stack: ${stack_name}"
   if build_stack_custom_image "${stack_dir}"; then
     show_warning_and_wait "Custom image build finished successfully for stack: ${stack_name}" 3
+    refresh_stack_generated_compose_with_feedback "${stack_dir}" || true
     return 0
   else
     build_image_status=$?
diff --git a/scripts/easy-docker/lib/app/wizard/flows/manage/docker.sh b/scripts/easy-docker/lib/app/wizard/flows/manage/docker.sh
deleted file mode 100755
index 6ef17921..00000000
--- a/scripts/easy-docker/lib/app/wizard/flows/manage/docker.sh
+++ /dev/null
@@ -1,81 +0,0 @@
-#!/usr/bin/env bash
-
-refresh_stack_generated_compose_with_feedback() {
-  local stack_dir="${1}"
-  local generated_compose_path=""
-  local render_compose_status=0
-
-  generated_compose_path="$(get_stack_generated_compose_path "${stack_dir}")"
-  if render_stack_compose_from_metadata "${stack_dir}"; then
-    show_warning_and_wait "Generated compose refreshed successfully: ${generated_compose_path}" 3
-    return 0
-  fi
-
-  render_compose_status=$?
-  show_warning_and_wait "The image build succeeded, but generated compose could not be refreshed (${render_compose_status}) for ${generated_compose_path}." 4
-  return "${render_compose_status}"
-}
-
-run_build_stack_custom_image_with_feedback() {
-  local stack_name="${1}"
-  local stack_dir="${2}"
-  local build_image_status=0
-
-  show_warning_message "Starting docker build for stack: ${stack_name}"
-  if build_stack_custom_image "${stack_dir}"; then
-    show_warning_and_wait "Custom image build finished successfully for stack: ${stack_name}" 3
-    refresh_stack_generated_compose_with_feedback "${stack_dir}" || true
-    return 0
-  else
-    build_image_status=$?
-  fi
-  case "${build_image_status}" in
-  11)
-    show_warning_and_wait "Custom image build failed: missing metadata.json in ${stack_dir}." 4
-    ;;
-  12)
-    show_warning_and_wait "Custom image build failed: stack env file not found in ${stack_dir}." 4
-    ;;
-  13)
-    show_warning_and_wait "Custom image build failed: CUSTOM_IMAGE is missing in stack env file." 4
-    ;;
-  14)
-    show_warning_and_wait "Custom image build failed: CUSTOM_TAG is missing in stack env file." 4
-    ;;
-  15)
-    show_warning_and_wait "Custom image build failed: frappe_branch missing in metadata.json." 4
-    ;;
-  16)
-    show_warning_and_wait "Custom image build failed: could not generate apps.json from metadata app selection." 4
-    ;;
-  17)
-    show_warning_and_wait "Custom image build failed: apps.json not found after generation." 4
-    ;;
-  18)
-    show_warning_and_wait "Custom image build failed: base64 command is not available in this environment." 4
-    ;;
-  19)
-    show_warning_and_wait "Custom image build failed: apps.json could not be base64-encoded." 4
-    ;;
-  20)
-    show_warning_and_wait "Custom image build failed: images/layered/Containerfile not found." 4
-    ;;
-  21)
-    show_warning_and_wait "Custom image build failed: docker build returned an error. Check the output above." 4
-    ;;
-  22)
-    show_warning_and_wait "Custom image build failed: git is required for app branch precheck (git ls-remote)." 4
-    ;;
-  23)
-    show_warning_and_wait "Custom image build failed: could not parse app entries from apps.json." 4
-    ;;
-  24)
-    show_warning_and_wait "Custom image build failed: app branch precheck failed -> ${EASY_DOCKER_BUILD_ERROR_DETAIL}" 6
-    ;;
-  *)
-    show_warning_and_wait "Custom image build failed (${build_image_status})." 4
-    ;;
-  esac
-
-  return "${build_image_status}"
-}