This paper introduces an open source, interoperable generic software tool set catering for the entire workflow of creation, migration, annotation, query and analysis of multi-layer linguistic corpora. It consists of four components: Salt, a graph-based meta model and API for linguistic data, the common data model for the rest of the tool set; Pepper, a conversion tool and platform for linguistic data that can be used to convert many different linguistic formats into each other; Atomic, an extensible, platform-independent multi-layer desktop annotation software for linguistic corpora; ANNIS, a search and visualization architecture for multi-layer linguistic corpora with many different visualizations and a powerful native query language. The set was designed to solve the following issues in a multi-layer corpus workflow: Lossless data transition between tools through a common data model generic enough to allow for a potentially unlimited number of different types of annotation, conversion capabilities for different linguistic formats to cater for the processing of data from different sources and/or with existing annotations, a high level of extensibility to enhance the sustainability of the whole tool set, analysis capabilities encompassing corpus and annotation query alongside multi-faceted visualizations of all annotation layers.