Give Claude Code some guidelines

CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+LabKey Server is a large Java web application platform for biomedical research data management. It uses a modular monolith architecture with 150+ Gradle modules, built on Spring Boot 4 / Spring Framework 7 with embedded Tomcat 11. It targets Java 25 and supports both PostgreSQL and MS SQL Server databases.
+
+## Build Commands
+
+```bash
+# Configure IntelliJ IDEA project files
+./gradlew ijConfigure
+
+# Select database (populates application.properties from templates)
+./gradlew pickPg          # PostgreSQL
+./gradlew pickMssql       # MS SQL Server
+
+# Build and deploy to embedded Tomcat
+./gradlew deployApp
+
+# Build a specific module
+./gradlew :server:modules:platform:core:build
+
+# Build with a predefined module set
+./gradlew -PmoduleSet=community build
+
+# Exclude test modules for faster builds
+./gradlew -PexcludeTestModules build
+
+# Build a distribution
+./gradlew -PmoduleSet=distributions :distributions:base:dist
+```
+
+## Running Tests
+
+**Unit tests** are static `TestCase` inner classes within production source files. They are registered via the module's `getUnitTests()` method and run within the server JVM.
+
+**Integration tests** require a running server and database. They are registered via `getIntegrationTests()`.
+
+**Selenium UI tests** (in `server/testAutomation/`):
+```bash
+./gradlew :server:testAutomation:initProperties    # Generate test.properties
+./gradlew :server:testAutomation:uiTests -Psuite=DRT   # Run a test suite
+```
+UI tests require a running LabKey server, a browser driver (ChromeDriver or Geckodriver) on PATH, and configured `test.properties`.
+
+## Architecture
+
+### Module System
+
+Each module lives under `server/modules/` and contains:
+- `module.properties` — metadata including `ModuleClass`, `SchemaVersion`, `SupportedDatabases`
+- `build.gradle` — uses `org.labkey.build.module` plugin
+- A module class extending `SpringModule` (which extends `DefaultModule` implementing `Module`)
+
+Module lifecycle methods in order: `init()` → `versionUpdate()` → `afterUpdate()` → `startup()` → `startupAfterSpringConfig()` → `startBackgroundThreads()` → `destroy()`
+
+In `init()`, modules register controllers via `addController("name", Controller.class)` and set up service implementations. Controllers follow the pattern `*Controller.java`.
+
+### Core Platform Modules (`server/modules/platform/`)
+
+The `api` module provides the core framework (Module interface, SpringModule base class, services, utilities). Other key platform modules: `core` (auth, security, admin), `query` (SQL engine), `experiment`, `study`, `assay`, `pipeline` (job processing), `search`, `audit`, `visualization`.
+
+### Entry Point
+
+`server/embedded/src/org/labkey/embedded/LabKeyServer.java` — a `@SpringBootApplication` that configures embedded Tomcat, SSL/TLS, Content Security Policy, and Log4J2.
+
+### Database
+
+Dual database support (PostgreSQL and MS SQL Server). Configuration lives in `server/configs/application.properties`, populated by `pickPg`/`pickMssql` tasks from `pg.properties`/`mssql.properties` templates. Each module declares its `SchemaVersion` in `module.properties` and manages its own schema migrations.
+
+### Frontend
+
+Mix of JSPs, React (via `@labkey/components`), and ExtJS. Modules with JavaScript/TypeScript have their own `package.json` and use npm builds. Node.js and npm versions are pinned in `gradle.properties` and downloaded during build.
+
+### Distributions
+
+The `distributions/` directory defines 60+ distribution configurations that select which modules to package. Distributions inherit from each other (most inherit from `:distributions:base`). Distribution directory names must not collide with module names.
+
+### Dependency Management
+
+All external library versions are centralized in `gradle.properties` (200+ version properties). The root `build.gradle` forces consistent versions across all modules via `resolutionStrategy`. Always consult before adding, removing, or updating a third-party dependency.
+
+## Coding Conventions
+
+- **Java Streams**: Prefer `Stream` API over traditional for-loops for collection processing.
+- **Resources**: Use try-with-resources for automatic resource management.
+- **Nullability**: Use `org.jetbrains.annotations.NotNull` and `@Nullable`. Be explicit in public API signatures.
+- **Logging**: Use Log4J2. Name the static logger `LOG`, initialized via `LogHelper.getLogger()`:
+  ```java
+  private static final Logger LOG = LogHelper.getLogger(MyClass.class, "optional description");
+  ```
+- **Unit tests**: Create a static `TestCase` inner class extending `Assert` in the same file as production code. Use JUnit 4 annotations (`@Test`). Register new test classes in the owning module's `getUnitTests()`.
+- **Selenium tests**: Subclass `BaseWebDriverTest`. Use a `@BeforeClass` for setup and override `doCleanup()` for cleanup. See `SecurityTest` as an example.
+- **Formatting**: Follow IntelliJ IDEA project settings in `.idea/codeStyles/Project.xml`.
+
+## Key Build Properties (`gradle.properties`)
+
+- `sourceCompatibility`/`targetCompatibility`: Java 25
+- `buildFromSource`: true (build modules from source vs. pulling artifacts)
+- `useLocalBuild`: use locally built artifacts
+- `moduleSet`: select a predefined set of modules (e.g., `community`, `all`, `distributions`)
+- `excludedModules`: comma-separated list of modules to exclude
+
+## Search Tips
+
+When searching for Java method usages, always include `*.jsp` and `*.jspf` files in addition to `*.java`. JSP files contain inline Java code and are significant callers of API methods (especially anything in `JspBase`).
+
+## Pull Request Format
+
+PRs should include sections for: **Rationale** (why the change is needed), **Related Pull Requests**, and **Changes** (notable items).