refactor(pipeline): restructure config, add PromptDirectory, consolidate SQLite layer (#217)

* Refactor ApplicationOptions to separate config concerns

* add prompt dir app option

* readability updates: remove magic numbers, update comments

* codebase formatting

* Update docs

* Extract argument parsing, timer out of

tooling/pipeline/src/services/prompt_directory.cc

@@ -0,0 +1,85 @@
+/**
+ * @file services/prompt_directory.cc
+ * @brief PromptDirectory implementation: validates the directory at
+ * construction and loads named prompt files on demand with in-process caching.
+ */
+
+#include "services/prompt_directory.h"
+
+#include <spdlog/spdlog.h>
+
+#include <filesystem>
+#include <fstream>
+#include <stdexcept>
+#include <string>
+#include <string_view>
+
+// ---------------------------------------------------------------------------
+// PromptDirectory
+// ---------------------------------------------------------------------------
+
+PromptDirectory::PromptDirectory(const std::filesystem::path& prompt_dir)
+    : prompt_dir_(prompt_dir) {
+  std::error_code ec;
+
+  // Scenario 4: directory must exist.
+  if (!std::filesystem::exists(prompt_dir_, ec) || ec) {
+    throw std::runtime_error(
+        "PromptDirectory: prompt directory does not exist: " +
+        prompt_dir_.string());
+  }
+
+  // Scenario 4: path must be a directory, not a file.
+  if (!std::filesystem::is_directory(prompt_dir_, ec) || ec) {
+    throw std::runtime_error(
+        "PromptDirectory: prompt directory path is not a directory: " +
+        prompt_dir_.string());
+  }
+
+  // Scenario 4: directory must be readable (probe with directory_iterator).
+  std::filesystem::directory_iterator probe(prompt_dir_, ec);
+  if (ec) {
+    throw std::runtime_error(
+        "PromptDirectory: prompt directory is not readable: " +
+        prompt_dir_.string() + " (" + ec.message() + ")");
+  }
+
+  spdlog::info("[PromptDirectory] Resolved prompt directory: {}",
+               prompt_dir_.string());
+}
+
+std::string PromptDirectory::Load(std::string_view key) {
+  const std::string key_str(key);
+
+  // Return cached content if already loaded during this run.
+  const auto cache_it = cache_.find(key_str);
+  if (cache_it != cache_.end()) {
+    return cache_it->second;
+  }
+
+  // Scenario 3: resolve <prompt_dir>/<key>.md and require it to exist.
+  const std::filesystem::path file_path =
+      prompt_dir_ / std::filesystem::path(key_str + ".md");
+
+  std::ifstream file(file_path);
+  if (!file.is_open()) {
+    throw std::runtime_error(
+        "PromptDirectory: prompt file not found for key '" + key_str +
+        "': " + file_path.string());
+  }
+
+  std::string content((std::istreambuf_iterator<char>(file)),
+                      std::istreambuf_iterator<char>());
+  file.close();
+
+  if (content.empty()) {
+    throw std::runtime_error("PromptDirectory: prompt file for key '" +
+                             key_str + "' is empty: " + file_path.string());
+  }
+
+  spdlog::info("[PromptDirectory] Loaded prompt '{}' from '{}' ({} chars)",
+               key_str, file_path.string(), content.size());
+
+  cache_.emplace(key_str, content);
+  return content;
+}