fix: stop double-executing git clone / setup hooks via run()

run() re-splits its argument as a bare string with no eval, so any
call like run "git clone \"$url\" \"$dir\"" corrupts the quoted
arguments (embedded escaped quotes survive as literal characters,
e.g. git sees the protocol as '"https). Each of the 4 affected call
sites papered over this by following run() with a second, correctly
quoted manual execution of the same command - meaning every real run
double-executed (git clone twice, pip install -e twice, conda env
create twice), with the first, corrupted attempt's failure masked by
the working second attempt.

Fixed by dropping run() at these sites entirely and gating on
$dry_run directly with a single, properly quoted real execution path
(matches the pattern already used in the new model-cache-redirect
extra):
- lib/cf-apps.functions: install-cf-app's clone, provision-orchard-node's clone
- cf-apps/circuitforge-core.manifest: pip install -e setup hook
- cf-apps/kiwi.manifest: conda env create setup hook

Verified on sif via a scratch-dir harness (install-cf-app
circuitforge-core): first run now clones cleanly with no mangled-URL
error, second run correctly skips the clone and re-runs the
idempotent pip install; state.conf stays single-entry across both.

cf-apps/circuitforge-core.manifest

@@ -13,8 +13,11 @@ app_needs_core=false
 
 app_setup_bare_metal() {
   local dir="$1"
-  run "conda run -n ${app_conda_env} pip install -e \"${dir}\""
+  if [[ $dry_run == true ]]; then
-  if [[ $dry_run != true ]]; then
+    boxline "DryRun: conda run -n ${app_conda_env} pip install -e ${dir}"
+  else
+    # run() re-splits its argument as a bare string with no eval, which
+    # mangles the quoted path - execute directly instead.
     conda run -n "${app_conda_env}" pip install -e "${dir}"
   fi
 }

cf-apps/kiwi.manifest

@@ -24,8 +24,11 @@ app_setup_docker() {
 # the docs for the LLM backend choice rather than guessing one.
 app_setup_bare_metal() {
   local dir="$1"
-  run "conda env create -f \"${dir}/environment.yml\" -n \"${app_conda_env}\""
+  if [[ $dry_run == true ]]; then
-  if [[ $dry_run != true ]]; then
+    boxline "DryRun: conda env create -f ${dir}/environment.yml -n ${app_conda_env}"
+  else
+    # run() re-splits its argument as a bare string with no eval, which
+    # mangles the quoted paths - execute directly instead.
     conda env create -f "${dir}/environment.yml" -n "${app_conda_env}"
   fi
   boxline "${app_name}: conda env '${app_conda_env}' created. See docs/getting-started/installation.md and llm-setup.md for the remaining BYOK LLM backend setup (Ollama/vLLM/OpenAI/Anthropic)."

lib/cf-apps.functions

@@ -181,13 +181,15 @@ install-cf-app() {
   local clone_dir="${apps_base_dir}/${app_name}"
   if [ -d "$clone_dir" ]; then
     warn "${clone_dir} already exists, skipping clone (will not overwrite)"
+  elif [[ $dry_run == true ]]; then
+    boxline "DryRun: git clone --recurse-submodules ${repo_url} ${clone_dir}"
   else
+    # run() re-splits its argument as a bare string with no eval, which
+    # mangles anything with embedded quotes (URLs/paths) - execute directly
+    # instead, gated on $dry_run above rather than double-executing via run().
     boxline "Cloning ${app_name} from ${repo_url}"
-    run "git clone --recurse-submodules \"${repo_url}\" \"${clone_dir}\""
+    mkdir -p "$apps_base_dir"
-    if [[ $dry_run != true ]]; then
+    git clone --recurse-submodules "$repo_url" "$clone_dir"
-      mkdir -p "$apps_base_dir"
-      git clone --recurse-submodules "$repo_url" "$clone_dir"
-    fi
   fi
 
   if [ -n "$app_env_template" ] && [ -f "${clone_dir}/${app_env_template}" ] && [ ! -f "${clone_dir}/.env" ]; then
@@ -260,13 +262,13 @@ provision-orchard-node() {
 
   if [ -d "$clone_dir" ]; then
     warn "${clone_dir} already exists, skipping clone (will not overwrite)"
+  elif [[ $dry_run == true ]]; then
+    boxline "DryRun: git clone ${repo_url} ${clone_dir}"
   else
+    # See install-cf-app for why this doesn't route through run().
     boxline "Cloning circuitforge-orch from Forgejo"
-    run "git clone \"${repo_url}\" \"${clone_dir}\""
+    mkdir -p "$apps_base_dir"
-    if [[ $dry_run != true ]]; then
+    git clone "$repo_url" "$clone_dir"
-      mkdir -p "$apps_base_dir"
-      git clone "$repo_url" "$clone_dir"
-    fi
   fi
 
   boxline "Handing off to circuitforge-orch's own install.sh..."