Add many integration tests, including necessary configuration to fetch test data from S3-hosted Maven repository

Begin sketching out basic IT for SearchToBLIB#convert

Implement generation of (empty) job data.

Add basic assertions to the still-failing IT.

Flesh out remaining permutations as separate test cases.

Generate data and ensure setup is appropriate.

Fix mock sequence generation.

Begin exploring running SeachToBLIBIT against real output files.

Begin cleaning up test code and issues, getting them to run against test data.

Make basic changes to adapt other test cases.

Fix up BLIB assertions.

Force test-created percolator file data objects to contain a percolator version, and assert it's used when exporting a single sample ELIB.

Clean up use of reflection in IT by making package-private method instead protected.

Change SearchToBLIBIT over to using encyclopedia results from a better test dataset that's been subsetted to be very small but still slightly interesting.

SearchToBLIB test now refers to classpath resources.

Move resources to setup, destroy in teardown

Created stub for end-to-end pipeline, fixed suffixes for SearchToBLIBIT

Fixed suffixes on BLIB test

Point several ITs to new resource locations. Improve assertions. Begin documenting and standardizing behavior of converters w.r.t. resource cleanup.

Clean up test failures, including one due to a bad grep determining the expected value.

Update tests to use new files in updated test data JAR.

Added some more relevant assertions

Revise set of test resources and update tests appropriately.

Final update to get tests passing with additional dummy FASTA test resource.

Better assertions on individual searches, still trying to understand the entry points for the export code

Add workaround for headless Java 8 builds.

Passing all tests with different assertions now.

Clean up workaround code and log a message.

Revert changes to main class

Relaxed ceilings of tests to maximum possible

Factor out static assertion method

Move tempReport also to setUp/tearDown

Update to use new resources for final ITs.

Skeleton of Xcordia test

Extract superclass for integration tests

Changed percolator threshold back down to 0.25

Fix up MS2PIPReaderIT with FASTA and entry count assertion.

Add assertions where we expect a valid but empty library.

Add assertion for empty BLIB.

Ensure that tests reopen closed library files before checking entry counts.

Memoize abstract end to end IT

Memoize End-to-end IT

Simplify parameter setup for XCorDIA

Add S3-hosted Maven repo and S3 Wagon configuration.