# Onboard to an Unfamiliar Java Codebase with Atlas (2026)

> Atlas onboards you to an unfamiliar Java repo by asking codebase_search a plain-language question, then mapping the Maven module layout with glob.

Atlas helps you onboard to an unfamiliar Java codebase by starting from meaning rather than filenames. You ask codebase_search a plain-language question such as how requests are authenticated, and the semantic index returns ranked snippets with file paths from deep inside src/main/java. glob then maps the module layout so you see the shape of the Maven build before opening anything, read pulls only the two or three files that matter, and the lsp tool's goToDefinition operation follows the class hierarchy. Heavy fan-out goes to the explore subagent, which is permissioned read-only.

## Key takeaways

- codebase_search answers plain-language questions about a Java repo with ranked snippets and file paths, so you never start by guessing at package names.
- glob maps the Maven module layout and the src/main/java convention before you open a single class.
- The explore subagent is deny-by-default and only allows grep, glob, read, bash, webfetch, and websearch, so fan-out cannot edit your Java code.
- The lsp tool's goToDefinition operation walks a Java class hierarchy from interface to abstract base to implementation.
- A todowrite list carries open questions forward, and JUnit 5 via mvn test gives you a working baseline on day one.

## Where do I start in a Java repo I have never seen?

Start with a question, not a file. Ask codebase_search a plain-language question, for example how requests are authenticated, and Atlas queries the semantic index and returns ranked snippets with file paths. In a 2026 Maven project with six modules, that beats opening pom.xml and guessing.

The instinct in an unfamiliar Java repository is to open the pom.xml, read the module list, then start clicking down through src/main/java until something looks important. That approach scales badly, because Java package trees are deep and the class that matters is rarely the one with the obvious name. Atlas starts from meaning. Atlas searches code with hybrid semantic and keyword retrieval fused by reciprocal rank fusion, and Atlas indexes code by AST declarations using tree-sitter, not blind line windows, so the ranked snippets you get back are whole class and method declarations you can actually read, not arbitrary slices of a file.

## How do I see the shape of a multi-module Maven project quickly?

Run glob on the top-level directories. Atlas uses glob to reveal the package layout and naming conventions before opening anything, which in a Maven project means seeing each module, its 2 source roots, src/main/java and src/test/java, and where the pom.xml or build.gradle sits. JUnit 5 tests live under the test root.

The directory shape tells you things no single file will. A Java repository with four sibling modules and one that every other module depends on has an obvious center of gravity, and glob shows it in one call. Seeing that tests live under src/test/java in every module tells you where JUnit tests belong when you eventually write one. Seeing a module with a pom.xml and another with a build.gradle tells you the build story is not uniform, which is exactly the kind of thing that ambushes a new joiner on day three. Atlas maps the shape first, then reads.

## How does the Atlas explore subagent read a Java repo safely?

Delegate wide sweeps to the Atlas explore subagent through the task tool. The explore subagent runs a deny-by-default permission set that allows exactly 6 tools, grep, glob, read, bash, webfetch, and websearch, so it cannot change a single Java file while it maps your Maven modules.

Onboarding involves a lot of looking, and looking is exactly the work you want to fan out. Atlas fans out work to subagents that can run in the foreground or in parallel background sessions, so a broad sweep across six Maven modules does not have to be serialized through your own reading. The safety property is what makes delegating comfortable: the explore subagent's permission set is deny-by-default, so an agent surveying your Java code physically cannot edit a class, touch a pom.xml, or run a build that mutates target output beyond what bash is permitted to do. Every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs.

## How do I follow a Java class hierarchy while onboarding?

Read the 2 or 3 files codebase_search ranked highest, then follow imports with the lsp tool's goToDefinition operation. In Java, where a behavior is often split across an interface, an abstract base class, and a concrete implementation, goToDefinition is how you traverse the hierarchy instead of grepping for class names.

Reading three well-chosen Java files teaches you more than skimming thirty. codebase_search picks the three by relevance, and the lsp tool then lets you walk outward along the real symbol edges: from the interface the class implements, to the abstract parent it extends, to the collaborator it injects. That traversal is the mental model you are trying to build. Recording it as you go matters too, which is why Atlas records what you learned as a todowrite list, so the open questions survive into the next turn instead of evaporating when the session context rolls over.

## How do I confirm my understanding of a new Java codebase?

Run the tests. In a Java project, that means JUnit 5 via mvn test, with Maven resolving the classpath from the pom.xml. Watching a suite pass on a repo you just met in 2026 tells you the build works, the dependencies resolve, and your mental model has something to check itself against.

Onboarding ends when you can make a change and know whether you broke something. Running JUnit 5 via mvn test on day one establishes the baseline. Spotless is the formatter, so when you finally do write code, the diff you produce matches house style rather than starting a formatting argument in review. Maven is the package manager, so a dependency question has an answer in the pom.xml rather than in tribal memory. Atlas reads git branches, status, and diffs, so the recent history of the Java modules you are learning is available as context rather than as folklore.

## Steps

1. Run atlas in a project with a pom.xml or build.gradle and let it read your packages, classpath, and build configuration.
2. Ask codebase_search a plain-language question, for example how requests are authenticated; it queries the semantic index and returns ranked snippets with file paths.
3. Run glob on the top-level directories to see the Maven module layout and the src/main/java and src/test/java split before opening anything.
4. Read the two or three Java files codebase_search ranked highest, rather than skimming the whole package tree.
5. Follow imports and the class hierarchy with the lsp tool's goToDefinition operation, from interface to abstract base class to concrete implementation.
6. Delegate wide sweeps to the explore subagent through the task tool, which has a deny-by-default permission set allowing only grep, glob, read, bash, webfetch, and websearch.
7. Record what you learned as a todowrite list so the open questions survive into the next turn.
8. Establish a baseline by running JUnit 5 via mvn test, and format your first contribution with Spotless.

## FAQ

### fastest way to understand a large java codebase

Ask Atlas a plain-language question and let codebase_search query the semantic index for ranked snippets with file paths, then run glob to see the Maven module layout, read the top two or three classes, and follow the hierarchy with the lsp tool's goToDefinition operation.

### can an ai agent explore my java repo without changing anything

Yes. The Atlas explore subagent is defined with a deny-by-default permission set that only allows grep, glob, read, bash, webfetch, and websearch, so it cannot edit a class or touch your pom.xml while it surveys the repo.

### how do i map a multi-module maven project

Run glob on the top-level directories with Atlas to see the module layout, the pom.xml or build.gradle in each module, and the src/main/java and src/test/java split, before opening any individual Java file.

### how does atlas find code when i do not know the class name

Atlas queries the semantic index with codebase_search, which returns ranked snippets with file paths even when your words never appear in the source. Atlas indexes code by AST declarations using tree-sitter, so hits land on real Java declarations.

### how do i keep onboarding notes across ai sessions

Record what you learned as a todowrite list in Atlas so the open questions survive into the next turn. The list travels with the session rather than living in your head while you read another Java module.

### what should i run first in an unfamiliar java project

Run JUnit 5 via mvn test to establish a baseline. A passing suite proves the Maven build resolves the classpath from the pom.xml and gives you something to check a first change against. Format anything you write with Spotless.

### does atlas run parallel agents when exploring a codebase

Atlas fans out work to subagents that can run in the foreground or in parallel background sessions. Wide sweeps across Java modules go to the explore subagent through the task tool, which is permissioned read-only.

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