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/main.cc

@@ -9,6 +9,7 @@
 #include <boost/di.hpp>
 #include <boost/program_options.hpp>
 #include <chrono>
+#include <cstdint>
 #include <exception>
 #include <memory>
 #include <optional>
@@ -23,127 +24,14 @@
 #include "llama_backend_state.h"
 #include "services/enrichment_service.h"
 #include "services/export_service.h"
+#include "services/prompt_directory.h"
 #include "services/sqlite_export_service.h"
+#include "services/timer.h"
 #include "services/wikipedia_service.h"
 #include "web_client/curl_web_client.h"
 
-namespace prog_opts = boost::program_options;
 namespace di = boost::di;
 
-/**
- * @brief Parse command-line arguments into ApplicationOptions.
- *
- * @param argc Command-line argument count.
- * @param argv Command-line arguments.
- * @return Parsed ApplicationOptions if parsing succeeded, std::nullopt
- * otherwise.
- */
-std::optional<ApplicationOptions> ParseArguments(const int argc, char** argv) {
-  prog_opts::options_description desc("Pipeline Options");
-
-  auto opt = desc.add_options();
-
-  opt("help,h", "Produce help message");
-
-  opt("mocked", prog_opts::bool_switch(),
-      "Use mocked generator for brewery/user data");
-
-  opt("model,m", prog_opts::value<std::string>()->default_value(""),
-      "Path to LLM model (gguf)");
-
-  opt("temperature", prog_opts::value<float>()->default_value(1.0F),
-      "Sampling temperature (higher = more random)");
-
-  opt("top-p", prog_opts::value<float>()->default_value(0.95F),
-      "Nucleus sampling top-p in (0,1] (higher = more random)");
-
-  opt("top-k", prog_opts::value<uint32_t>()->default_value(64),
-      "Top-k sampling parameter (higher = more candidate tokens)");
-
-  opt("n-ctx", prog_opts::value<uint32_t>()->default_value(8192),
-      "Context window size in tokens (1-32768)");
-
-  opt("seed", prog_opts::value<int>()->default_value(-1),
-      "Sampler seed: -1 for random, otherwise non-negative integer");
-
-  // Handle the "no arguments" or "help" case
-  if (argc == 1) {
-    spdlog::info("Biergarten Pipeline");
-    std::stringstream usage_stream;
-    usage_stream << "\nUsage: biergarten-pipeline [options]\n\n" << desc;
-    spdlog::info(usage_stream.str());
-    return std::nullopt;
-  }
-
-  try {
-    prog_opts::variables_map variables_map;
-    prog_opts::store(prog_opts::parse_command_line(argc, argv, desc),
-                     variables_map);
-    prog_opts::notify(variables_map);
-
-    if (variables_map.contains("help")) {
-      std::stringstream help_stream;
-      help_stream << "\n" << desc;
-      spdlog::info(help_stream.str());
-      return std::nullopt;
-    }
-
-    const auto use_mocked = variables_map["mocked"].as<bool>();
-    const auto model_path = variables_map["model"].as<std::string>();
-
-    if (use_mocked && !model_path.empty()) {
-      spdlog::error(
-          "Invalid arguments: --mocked and --model are mutually exclusive");
-      return std::nullopt;
-    }
-
-    if (!use_mocked && model_path.empty()) {
-      spdlog::error(
-          "Invalid arguments: Either --mocked or --model must be specified");
-      return std::nullopt;
-    }
-
-    const bool has_llm_params = !variables_map["temperature"].defaulted() ||
-                                !variables_map["top-p"].defaulted() ||
-                                !variables_map["top-k"].defaulted() ||
-                                !variables_map["seed"].defaulted();
-
-    if (use_mocked && has_llm_params) {
-      spdlog::warn(
-          "Sampling parameters (--temperature, --top-p, --top-k, --seed) are"
-          " ignored when using --mocked");
-    }
-
-    ApplicationOptions options;
-    options.use_mocked = use_mocked;
-    options.model_path = model_path;
-    options.temperature = variables_map["temperature"].as<float>();
-    options.top_p = variables_map["top-p"].as<float>();
-    options.top_k = variables_map["top-k"].as<uint32_t>();
-    options.n_ctx = variables_map["n-ctx"].as<uint32_t>();
-    options.seed = variables_map["seed"].as<int>();
-
-    return options;
-  } catch (const std::exception& exception) {
-    spdlog::error("Failed to parse command-line arguments: {}",
-                  exception.what());
-    return std::nullopt;
-  } catch (...) {
-    spdlog::error("Failed to parse command-line arguments: unknown error");
-    return std::nullopt;
-  }
-}
-
-struct Timer {
-  std::chrono::steady_clock::time_point start_time =
-      std::chrono::steady_clock::now();
-  [[nodiscard]] int64_t Elapsed() const {
-    return std::chrono::duration_cast<std::chrono::milliseconds>(
-               std::chrono::steady_clock::now() - start_time)
-        .count();
-  }
-};
-
 int main(const int argc, char** argv) {
   try {
     Timer timer;
@@ -157,6 +45,20 @@ int main(const int argc, char** argv) {
     }
 
     const auto options = *parsed_options;
+    const std::string model_path = options.generator.model_path.string();
+    const auto sampling =
+        options.generator.sampling.value_or(SamplingOptions{});
+
+    std::unique_ptr<IPromptDirectory> prompt_directory;
+    if (!options.generator.use_mocked) {
+      try {
+        prompt_directory =
+            std::make_unique<PromptDirectory>(options.pipeline.prompt_dir);
+      } catch (const std::exception& dir_error) {
+        spdlog::error("[Startup] Invalid --prompt-dir: {}", dir_error.what());
+        return 1;
+      }
+    }
 
     const auto injector = di::make_injector(
         di::bind<WebClient>().to<CURLWebClient>(),
@@ -164,10 +66,11 @@ int main(const int argc, char** argv) {
         di::bind<IEnrichmentService>().to<WikipediaService>(),
         di::bind<IExportService>().to<SqliteExportService>(),
         di::bind<IPromptFormatter>().to<Gemma4JinjaPromptFormatter>(),
-        di::bind<std::string>().to(options.model_path),
+        di::bind<std::string>().to(model_path),
         di::bind<DataGenerator>().to(
-            [options](const auto& inj) -> std::unique_ptr<DataGenerator> {
-              if (options.use_mocked) {
+            [options, model_path, sampling, &prompt_directory](
+                const auto& inj) -> std::unique_ptr<DataGenerator> {
+              if (options.generator.use_mocked) {
                 spdlog::info(
                     "[Generator] Using MockGenerator (no model path provided)");
                 return std::make_unique<MockGenerator>();
@@ -176,9 +79,12 @@ int main(const int argc, char** argv) {
               spdlog::info(
                   "[Generator] Using LlamaGenerator: {} (temperature={}, "
                   "top-p={}, top-k={}, n_ctx={}, seed={})",
-                  options.model_path, options.temperature, options.top_p,
-                  options.top_k, options.n_ctx, options.seed);
-              return inj.template create<std::unique_ptr<LlamaGenerator>>();
+                  model_path, sampling.temperature, sampling.top_p,
+                  sampling.top_k, sampling.n_ctx, sampling.seed);
+              return std::make_unique<LlamaGenerator>(
+                  options, model_path,
+                  inj.template create<std::unique_ptr<IPromptFormatter>>(),
+                  std::move(prompt_directory));
             }));
 
     auto generator =