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/sqlite/helpers/sqlite_connection_helpers.cc

@@ -0,0 +1,66 @@
+#include "services/sqlite_connection_helpers.h"
+
+#include <stdexcept>
+
+namespace sqlite_export_service_internal {
+
+void SqliteDatabaseDeleter::operator()(sqlite3* handle) const noexcept {
+  if (handle != nullptr) {
+    sqlite3_close(handle);
+  }
+}
+
+void SqliteStatementDeleter::operator()(
+    sqlite3_stmt* statement) const noexcept {
+  if (statement != nullptr) {
+    sqlite3_finalize(statement);
+  }
+}
+
+void ThrowSqliteError(sqlite3* db_handle, std::string_view action) {
+  const std::string message =
+      db_handle != nullptr ? sqlite3_errmsg(db_handle) : "unknown SQLite error";
+  throw std::runtime_error(std::string(action) + ": " + message);
+}
+
+SqliteDatabaseHandle OpenDatabase(const std::filesystem::path& path) {
+  sqlite3* raw_handle = nullptr;
+  const int result = sqlite3_open(path.string().c_str(), &raw_handle);
+
+  SqliteDatabaseHandle handle(raw_handle);
+  if (result != SQLITE_OK) {
+    const std::string message = raw_handle != nullptr
+                                    ? sqlite3_errmsg(raw_handle)
+                                    : "unknown SQLite error";
+    throw std::runtime_error("Failed to open SQLite export database: " +
+                             message);
+  }
+
+  return handle;
+}
+
+void ExecSql(const SqliteDatabaseHandle& db_handle, std::string_view sql,
+             const char* action) {
+  char* error_message = nullptr;
+  const std::string sql_text(sql);
+  const int result = sqlite3_exec(db_handle.get(), sql_text.c_str(), nullptr,
+                                  nullptr, &error_message);
+  if (result != SQLITE_OK) {
+    const std::string message = error_message != nullptr
+                                    ? error_message
+                                    : sqlite3_errmsg(db_handle.get());
+    sqlite3_free(error_message);
+    throw std::runtime_error(std::string(action) + ": " + message);
+  }
+}
+
+void RollbackTransactionNoThrow(
+    const SqliteDatabaseHandle& db_handle) noexcept {
+  if (!db_handle) {
+    return;
+  }
+
+  sqlite3_exec(db_handle.get(), "ROLLBACK;", nullptr, nullptr, nullptr);
+}
+
+}  // namespace sqlite_export_service_internal