add required bookdown files

Author: kimberlyh66

_bookdown.yml

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+rmd_subdir: true
+rmd_files: ["index.Rmd", "README.Rmd", "data-sources.Rmd", 
+"software.Rmd", "scientific-objectives-and-experimental-design/README.Rmd",
+"scientific-objectives-and-experimental-design/protocols/README.Rmd",
+"scientific-objectives-and-experimental-design/protocols/controlled-environment-protocols.Rmd",
+"scientific-objectives-and-experimental-design/protocols/manual-field-data-protocols.Rmd",
+"scientific-objectives-and-experimental-design/protocols/phenotractor-protocols.Rmd",
+"scientific-objectives-and-experimental-design/protocols/sensor-calibration.Rmd",
+"scientific-objectives-and-experimental-design/protocols/template-protocol.Rmd",
+"scientific-objectives-and-experimental-design/protocols/uav-protocols.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/README.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth/README.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth/sorghum-lines-danforth.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/README.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1-continued.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-2.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-mac.Rmd",
+"user-manual/README.Rmd",
+"user-manual/what-data-is-available.Rmd",
+"user-manual/data-products/README.Rmd",
+"user-manual/data-products/environmental-conditions.Rmd",
+"user-manual/data-products/fluorescence-intensity-imaging.Rmd",
+"user-manual/data-products/genomics-data.Rmd",
+"user-manual/data-products/geospatial-information.Rmd",
+"user-manual/data-products/hyperspectral-imaging-data.Rmd",
+"user-manual/data-products/infrared-heat-imaging-data.Rmd",
+"user-manual/data-products/multispectral-imaging-data.Rmd",
+"user-manual/data-products/meteorological-data.Rmd",
+"user-manual/data-products/plantcv-trait-data.Rmd", 
+"user-manual/data-products/point-cloud-data.Rmd",
+"user-manual/how-to-access-data/README.Rmd",
+"user-manual/how-to-access-data/using-clowder-sensor-and-genoomics-data.Rmd",
+"user-manual/how-to-access-data/using-globus-sensor-and-genomics-data.Rmd",
+"user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata/README.Rmd",
+"user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata/accessing-betydb-via-arcmap-and-other-gis-software.Rmd",
+"user-manual/how-to-access-data/using-coge-genomics.Rmd",
+"user-manual/how-to-access-data/using-cyverse-genomics.Rmd",
+"user-manual/how-to-access-data/using-analysis-workbench-all-data.Rmd",
+"user-manual/data-use-policy.Rmd",
+"user-manual/manuscripts-and-authorship-guidelines.Rmd",
+"user-manual/release-reprocessing-schedule.Rmd",
+"technical-documentation/README.Rmd",
+"technical-documentation/data-standards/README.Rmd",
+"technical-documentation/data-standards/existing-data-standards.Rmd",
+"technical-documentation/data-standards/agronomic-and-phenotype-data-standards.Rmd",
+"technical-documentation/data-standards/genomic-data-standards.Rmd",
+"technical-documentation/data-standards/sensor-data-standards.Rmd",
+"technical-documentation/data-standards/data-standards-committee.Rmd",
+"technical-documentation/directory-structure.Rmd",
+"technical-documentation/data-storage.Rmd",
+"technical-documentation/data-transfer.Rmd",
+"technical-documentation/data-processing-pipeline/README.Rmd",
+"technical-documentation/data-processing-pipeline/geospatial-time-series-structure.Rmd",
+"technical-documentation/data-backup.Rmd",
+"technical-documentation/data-collection.Rmd",
+"technical-documentation/data-product-creation/README.Rmd",
+"technical-documentation/data-product-creation/genomic-data.Rmd",
+"technical-documentation/data-product-creation/hyperspectral-data.Rmd",
+"technical-documentation/quality-assurance-and-quality-control.Rmd",
+"developer-manual/README.Rmd",
+"developer-manual/submitting-data-to-clowder.Rmd",
+"developer-manual/submitting-data-to-betydb.Rmd",
+"developer-manual/submitting-data-to-coge.Rmd",
+"developer-manual/developing-clowder-extractors.Rmd",
+"tutorials.Rmd",
+"appendix/README.Rmd",
+"appendix/code-of-conduct.Rmd",
+"appendix/collaboration-tools.Rmd",
+"appendix/glossary.Rmd"]

_output.yml

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+bookdown::gitbook:
+  split_by: chapter

index.Rmd

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+---
+title: "TERRA REF"
+---