Add copilot-instructions.md and clarify Docker testing in AGENTS.md

Add .github/copilot-instructions.md for GitHub Copilot, mirroring
CLAUDE.md with a pointer to AGENTS.md for full project guidance.

Update AGENTS.md to document that source code changes under
src/viral_ngs/ require pip install -e inside the container, since
the package is pre-installed in the image and volume mounts alone
do not override Python imports.

Author: dpark01

.github/copilot-instructions.md

@@ -0,0 +1,31 @@
+# Copilot Instructions
+
+This file provides guidance to GitHub Copilot when working with code in this repository.
+
+**IMPORTANT**: Always read [AGENTS.md](../AGENTS.md) at the start of every session before doing any work. It contains comprehensive project context and development guidelines that are essential for working in this codebase.
+
+## Quick Reference
+
+- **Docker-centric development**: Run tests inside containers, not on host
+- **Import pattern**: `from viral_ngs import core` then `core.samtools.SamtoolsTool()`
+- **Test location**: `tests/unit/<module>/`
+- **Dependencies**: ALL via conda, not pip (see `docker/requirements/*.txt`)
+
+## Running Tests
+
+```bash
+docker run --rm \
+  -v $(pwd):/opt/viral-ngs/source \
+  quay.io/broadinstitute/viral-ngs:main-core \
+  pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit
+```
+
+## Key Files
+
+| File | Purpose |
+|------|---------|
+| [AGENTS.md](../AGENTS.md) | Full AI assistant guidance |
+| [pyproject.toml](../pyproject.toml) | Package configuration |
+| [docker/](../docker/) | Dockerfiles and requirements |
+| [src/viral_ngs/](../src/viral_ngs/) | Source code |
+| [tests/](../tests/) | Test files |

AGENTS.md

@@ -69,6 +69,21 @@ docker run --rm \
   pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit/classify
 ```
 
+**Important: Testing source code changes requires re-installing the package.**
+The `-v` mount makes your local files visible on disk, but `viral_ngs` is already installed as a package inside the container image. Python imports resolve to the *installed* copy, not your mounted source files. If you've modified files under `src/viral_ngs/`, you must re-install before running tests:
+
+```bash
+# Run tests with local source changes applied
+docker run --rm \
+  -v $(pwd):/opt/viral-ngs/source \
+  quay.io/broadinstitute/viral-ngs:main-core \
+  bash -c "pip install -e /opt/viral-ngs/source --quiet && pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit"
+```
+
+Changes to test files (`tests/`) and test inputs (`tests/input/`) are picked up automatically via the volume mount — the re-install is only needed when modifying the `src/viral_ngs/` package code.
+
+Running pytest directly on the host will generally not work — most dependencies (bioinformatics tools, conda packages) are only available inside the Docker containers. Always test inside Docker.
+
 **Test conventions:**
 - Uses pytest (not nose or unittest)
 - Test files in `tests/unit/<module>/`