fix: updated execute_command to not mangle heredocs and also added explicit instructions to the coder and sisyphus agents to use fs_write and fs_patch over execute_command when writing files

assets/functions/tools/execute_command.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -e
 
-# @describe Execute the shell command.
+# @describe Execute the shell command. DO NOT use this to write files — use fs_write (new files) or fs_patch (edits) instead. Shell-based file writes (cat >, echo >, printf >, tee, heredocs, python -c "open(...)") break on multi-line content, special characters, quoted strings, and nested language blocks.
 # @option --command! The command to execute.
 
 # @env LLM_OUTPUT=/dev/stdout The output path
@@ -11,6 +11,11 @@ source "$LLM_PROMPT_UTILS_FILE"
 
 main() {
     guard_operation
+    local script
+    script="$(mktemp)"
+    # shellcheck disable=SC2064
+    trap "rm -f '$script'" EXIT
     # shellcheck disable=SC2154
-    eval "$argc_command" >> "$LLM_OUTPUT"
+    printf '%s\n' "$argc_command" > "$script"
+    bash "$script" >> "$LLM_OUTPUT"
 }