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/includes/services/timer.h

@@ -0,0 +1,35 @@
+#ifndef BIERGARTEN_PIPELINE_INCLUDES_SERVICES_TIMER_H_
+#define BIERGARTEN_PIPELINE_INCLUDES_SERVICES_TIMER_H_
+
+#include <chrono>
+
+/**
+ * @file services/timer.h
+ * @brief Simple timer utility for measuring elapsed time.
+ */
+class Timer {
+  std::chrono::steady_clock::time_point start_time =
+      std::chrono::steady_clock::now();
+
+ public:
+  Timer(const Timer&) = delete;
+  Timer& operator=(const Timer&) = delete;
+  Timer(Timer&&) = delete;
+  Timer& operator=(Timer&&) = delete;
+  Timer() = default;
+  ~Timer() = default;
+
+  [[nodiscard]] int64_t Elapsed() const {
+    return std::chrono::duration_cast<std::chrono::milliseconds>(
+               std::chrono::steady_clock::now() - start_time)
+        .count();
+  }
+
+  [[nodiscard]] int64_t Reset() {
+    auto previous_elapsed = Elapsed();
+    start_time = std::chrono::steady_clock::now();
+    return previous_elapsed;
+  }
+};
+
+#endif  // BIERGARTEN_PIPELINE_INCLUDES_SERVICES_TIMER_H_