Add CLAUDE.md guidance for Claude Code

[denis-yuen]

Description
Adds a CLAUDE.md documenting the build/codegen flow (Swagger Codegen + javax→jakarta replacer + flatten-plugin generated/ output), dependency conventions, and PR/JIRA conventions carried over from dockstore/dockstore where applicable, for future Claude Code sessions working in this repo.

Review Instructions
No code changes, just a new documentation file — a quick read-through is sufficient.

Issue
N/A

Security and Privacy

• Check that you pass the basic style checks and unit tests by running mvn clean install
• Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
• Follow the existing JPA patterns for queries, using named parameters, to avoid SQL injection
• If you are changing dependencies, check the Snyk status check or the dashboard to ensure you are not introducing new high/critical vulnerabilities
• Assume that inputs to the API can be malicious, and sanitize and/or check for Denial of Service type values, e.g., massive sizes
• Do not serve user-uploaded binary images through the Dockstore API
• Ensure that endpoints that only allow privileged access enforce that with the @RolesAllowed annotation
• Do not create cookies, although this may change in the future
• If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

🤖 Generated with Claude Code