fix(manifest): preserve substituted file newlines

TODO.md

@@ -20,7 +20,7 @@
 - [ ] Make ordinary update dry-runs use the saved/current selection. Both menus bypass selection in dry-run and select every manifest entry, so the preview can diverge from the real update. (`scripts/lib/plugins.ps1:91`, `scripts/lib/plugins.sh:97`)
 - [ ] Reconcile resources whose ownership record remains but whose installation was removed manually. `ensure_cli()` and `ensure_mcporter()` return early from a ledger record without checking the actual CLI or server; normal sync cannot restore the missing resource. (`scripts/lib/managed-extensions.py:342`, `scripts/lib/managed-extensions.py:395`)
 - [ ] Update owned MCPorter itself on `--update`. `ensure_cli()` returns whenever its ledger record exists, so a selected MCPorter package never receives the requested update. (`scripts/lib/managed-extensions.py:342`)
-- [ ] Keep terminal newlines in Bash-managed files that need substitution. Command substitution strips trailing newlines before Bash hashes and writes the content, while PowerShell retains them; switching installers causes needless file changes and backups. (`scripts/lib/manifest.sh:70`, `scripts/lib/manifest.ps1:75`)
+- [x] Keep terminal newlines in Bash-managed files that need substitution. Command substitution strips trailing newlines before Bash hashes and writes the content, while PowerShell retains them; switching installers causes needless file changes and backups. (`scripts/lib/manifest.sh:70`, `scripts/lib/manifest.ps1:75`)
 - [ ] Parse the Bash plugin inventory as JSON and stop when listing fails. `plugin_installed()` searches for one exact spacing pattern and suppresses CLI errors; a minified response or listing failure marks installed plugins unchecked, allowing an update to remove owned plugins. PowerShell parses JSON and fails on a CLI error. (`scripts/lib/plugins.sh:4`, `scripts/lib/plugins.ps1:36`)
 - [x] Serialize Bash manifest entries without shell word splitting. `write_managed_manifest()` loops over command substitution; a managed filename containing spaces becomes multiple invalid entries and can no longer be reconciled correctly. (`scripts/lib/manifest.sh:47`)
 - [ ] Allow uninstall to reconcile owned extensions when file manifests are missing. Both uninstall commands stop with “Not installed” based only on destination manifests, even if `extensions.json` still owns plugins, skills, or MCP servers. (`scripts/commands/uninstall.ps1:21`, `scripts/commands/uninstall.sh:34`)

scripts/lib/manifest.sh

@@ -68,10 +68,12 @@ sync_managed_destination() {
     relative=${source_file#"$source/"}
     if [ "${destination##*/}" = .codex ] && [[ "$relative" = skills/* ]]; then continue; fi
     target="$destination/$relative"
-    content=$(<"$source_file")
+    content=$(cat -- "$source_file" && printf '\034') || return
+    content=${content%$'\034'}
     needs_sub=false
     if [ "$flashbang_enabled" = false ] && [[ "$relative" = settings.json || "$relative" = config.toml ]]; then
-      content=$(python3 "$(dirname -- "${BASH_SOURCE[0]}")/install-options.py" filter --path "$source_file" --flashbang false) || return
+      content=$(python3 "$(dirname -- "${BASH_SOURCE[0]}")/install-options.py" filter --path "$source_file" --flashbang false && printf '\034') || return
+      content=${content%$'\034'}
       needs_sub=true
     fi
     if [[ "$needs_sub" = true || "$content" == *'__AI_CONFIG_ROOT__'* || "$content" == *'__HOOK_COMMAND__'* || "$content" == *'__POWERSHELL_HOOK_COMMAND__'* || "$content" == *'__POWERSHELL_COMMAND__'* || "$content" == *'__CLAUDE_CODE_MAX_TOOL_USE_CONCURRENCY__'* ]]; then

scripts/tests/test-managed-install.sh

@@ -30,6 +30,11 @@ out2=$(sync_managed_destination "$source_dir" "$destination" run2 "$destination"
 [ -z "$(printf '%s\n' "$out2" | grep -v '^UNCHANGED' | grep -v '^SOURCE ')" ] || { printf 'Second identical install was not a no-op:\n%s\n' "$out2" >&2; exit 1; }
 [ ! -d "$destination/backups/run2" ] || { printf 'Idempotent install must not create a backup.\n' >&2; exit 1; }
 
+printf 'root=__AI_CONFIG_ROOT__\n\n' > "$source_dir/newlines.txt"
+printf 'root=%s\n\n' "$destination" > "$work/expected-newlines.txt"
+sync_managed_destination "$source_dir" "$destination" newlines "$destination" bash bash false > /dev/null
+cmp -s "$work/expected-newlines.txt" "$destination/newlines.txt" || { printf 'Substitution changed terminal newlines.\n' >&2; exit 1; }
+
 printf 'mine' > "$destination/foreign.md"
 
 rm -f "$source_dir/b.md" "$source_dir/c.md"