From e203f6738d3c5d9436c792276b9a6442e8a565f2 Mon Sep 17 00:00:00 2001
From: Zach Sents <zachsents@gmail.com>
Date: Mon, 11 Dec 2023 15:09:47 -0700
Subject: [PATCH] Restored standard directory structure for backend

---
 backend/WebContent/META-INF/MANIFEST.MF             |   2 ++
 .../WEB-INF}/lib/beam-core-0.9.2.jar                | Bin
 .../WEB-INF}/lib/beam-func-0.9.2.jar                | Bin
 .../WEB-INF}/lib/cdk-atomtype-1.5.14.jar            | Bin
 .../WEB-INF}/lib/cdk-core-1.5.14.jar                | Bin
 .../WEB-INF}/lib/cdk-data-1.5.14.jar                | Bin
 .../WEB-INF}/lib/cdk-interfaces-1.5.14.jar          | Bin
 .../{ => WebContent/WEB-INF}/lib/cdk-io-1.5.14.jar  | Bin
 .../WEB-INF}/lib/cdk-ioformats-1.5.14.jar           | Bin
 .../WEB-INF}/lib/cdk-isomorphism-1.5.14.jar         | Bin
 .../WEB-INF}/lib/cdk-smiles-1.5.14.jar              | Bin
 .../WEB-INF}/lib/cdk-standard-1.5.14.jar            | Bin
 .../WEB-INF}/lib/cdk-valencycheck-1.5.14.jar        | Bin
 .../WEB-INF}/lib/commons-codec-1.10.jar             | Bin
 .../WEB-INF}/lib/commons-codec-1.9.jar              | Bin
 .../WEB-INF}/lib/commons-io-1.3.2.jar               | Bin
 .../{ => WebContent/WEB-INF}/lib/commons-io-2.5.jar | Bin
 .../WEB-INF}/lib/commons-logging-1.2.jar            | Bin
 backend/{ => WebContent/WEB-INF}/lib/gson-2.7.jar   | Bin
 backend/{ => WebContent/WEB-INF}/lib/guava-17.0.jar | Bin
 .../WEB-INF}/lib/hamcrest-core-1.3.jar              | Bin
 .../WEB-INF}/lib/httpclient-4.5.1.jar               | Bin
 .../WEB-INF}/lib/httpclient-4.5.3.jar               | Bin
 .../{ => WebContent/WEB-INF}/lib/httpcore-4.4.3.jar | Bin
 .../{ => WebContent/WEB-INF}/lib/httpcore-4.4.6.jar | Bin
 .../{ => WebContent/WEB-INF}/lib/httpmime-4.5.4.jar | Bin
 .../WEB-INF}/lib/javassist-3.12.1.GA.jar            | Bin
 .../WEB-INF}/lib/javax.json-1.0.2.jar               | Bin
 backend/{ => WebContent/WEB-INF}/lib/jdom-1.1.jar   | Bin
 .../WEB-INF}/lib/joda-time-2.9.9.jar                | Bin
 .../WEB-INF}/lib/json-simple-1.1.1.jar              | Bin
 backend/{ => WebContent/WEB-INF}/lib/junit-4.12.jar | Bin
 .../libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar    | Bin
 ...libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old | Bin
 backend/{ => WebContent/WEB-INF}/lib/mxPdf.jar      | Bin
 .../{ => WebContent/WEB-INF}/lib/mxgraph-all.jar    | Bin
 .../WEB-INF}/lib/stax-utils-20070216.jar            | Bin
 .../{ => WebContent/WEB-INF}/lib/vecmath-1.5.2.jar  | Bin
 .../{ => WebContent/WEB-INF}/lib/xpp3-1.1.4c.jar    | Bin
 backend/{ => WebContent/WEB-INF}/web.xml            |   0
 40 files changed, 2 insertions(+)
 create mode 100644 backend/WebContent/META-INF/MANIFEST.MF
 rename backend/{ => WebContent/WEB-INF}/lib/beam-core-0.9.2.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/beam-func-0.9.2.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-atomtype-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-core-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-data-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-interfaces-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-io-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-ioformats-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-isomorphism-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-smiles-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-standard-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/cdk-valencycheck-1.5.14.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/commons-codec-1.10.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/commons-codec-1.9.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/commons-io-1.3.2.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/commons-io-2.5.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/commons-logging-1.2.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/gson-2.7.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/guava-17.0.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/hamcrest-core-1.3.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/httpclient-4.5.1.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/httpclient-4.5.3.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/httpcore-4.4.3.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/httpcore-4.4.6.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/httpmime-4.5.4.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/javassist-3.12.1.GA.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/javax.json-1.0.2.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/jdom-1.1.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/joda-time-2.9.9.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/json-simple-1.1.1.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/junit-4.12.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/mxPdf.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/mxgraph-all.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/stax-utils-20070216.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/vecmath-1.5.2.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/lib/xpp3-1.1.4c.jar (100%)
 rename backend/{ => WebContent/WEB-INF}/web.xml (100%)

diff --git a/backend/WebContent/META-INF/MANIFEST.MF b/backend/WebContent/META-INF/MANIFEST.MF
new file mode 100644
index 00000000..e41bf7bb
--- /dev/null
+++ b/backend/WebContent/META-INF/MANIFEST.MF
@@ -0,0 +1,2 @@
+Manifest-Version: 1.0
+Class-Path: 
\ No newline at end of file
diff --git a/backend/lib/beam-core-0.9.2.jar b/backend/WebContent/WEB-INF/lib/beam-core-0.9.2.jar
similarity index 100%
rename from backend/lib/beam-core-0.9.2.jar
rename to backend/WebContent/WEB-INF/lib/beam-core-0.9.2.jar
diff --git a/backend/lib/beam-func-0.9.2.jar b/backend/WebContent/WEB-INF/lib/beam-func-0.9.2.jar
similarity index 100%
rename from backend/lib/beam-func-0.9.2.jar
rename to backend/WebContent/WEB-INF/lib/beam-func-0.9.2.jar
diff --git a/backend/lib/cdk-atomtype-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-atomtype-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-atomtype-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-atomtype-1.5.14.jar
diff --git a/backend/lib/cdk-core-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-core-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-core-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-core-1.5.14.jar
diff --git a/backend/lib/cdk-data-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-data-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-data-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-data-1.5.14.jar
diff --git a/backend/lib/cdk-interfaces-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-interfaces-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-interfaces-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-interfaces-1.5.14.jar
diff --git a/backend/lib/cdk-io-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-io-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-io-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-io-1.5.14.jar
diff --git a/backend/lib/cdk-ioformats-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-ioformats-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-ioformats-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-ioformats-1.5.14.jar
diff --git a/backend/lib/cdk-isomorphism-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-isomorphism-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-isomorphism-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-isomorphism-1.5.14.jar
diff --git a/backend/lib/cdk-smiles-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-smiles-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-smiles-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-smiles-1.5.14.jar
diff --git a/backend/lib/cdk-standard-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-standard-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-standard-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-standard-1.5.14.jar
diff --git a/backend/lib/cdk-valencycheck-1.5.14.jar b/backend/WebContent/WEB-INF/lib/cdk-valencycheck-1.5.14.jar
similarity index 100%
rename from backend/lib/cdk-valencycheck-1.5.14.jar
rename to backend/WebContent/WEB-INF/lib/cdk-valencycheck-1.5.14.jar
diff --git a/backend/lib/commons-codec-1.10.jar b/backend/WebContent/WEB-INF/lib/commons-codec-1.10.jar
similarity index 100%
rename from backend/lib/commons-codec-1.10.jar
rename to backend/WebContent/WEB-INF/lib/commons-codec-1.10.jar
diff --git a/backend/lib/commons-codec-1.9.jar b/backend/WebContent/WEB-INF/lib/commons-codec-1.9.jar
similarity index 100%
rename from backend/lib/commons-codec-1.9.jar
rename to backend/WebContent/WEB-INF/lib/commons-codec-1.9.jar
diff --git a/backend/lib/commons-io-1.3.2.jar b/backend/WebContent/WEB-INF/lib/commons-io-1.3.2.jar
similarity index 100%
rename from backend/lib/commons-io-1.3.2.jar
rename to backend/WebContent/WEB-INF/lib/commons-io-1.3.2.jar
diff --git a/backend/lib/commons-io-2.5.jar b/backend/WebContent/WEB-INF/lib/commons-io-2.5.jar
similarity index 100%
rename from backend/lib/commons-io-2.5.jar
rename to backend/WebContent/WEB-INF/lib/commons-io-2.5.jar
diff --git a/backend/lib/commons-logging-1.2.jar b/backend/WebContent/WEB-INF/lib/commons-logging-1.2.jar
similarity index 100%
rename from backend/lib/commons-logging-1.2.jar
rename to backend/WebContent/WEB-INF/lib/commons-logging-1.2.jar
diff --git a/backend/lib/gson-2.7.jar b/backend/WebContent/WEB-INF/lib/gson-2.7.jar
similarity index 100%
rename from backend/lib/gson-2.7.jar
rename to backend/WebContent/WEB-INF/lib/gson-2.7.jar
diff --git a/backend/lib/guava-17.0.jar b/backend/WebContent/WEB-INF/lib/guava-17.0.jar
similarity index 100%
rename from backend/lib/guava-17.0.jar
rename to backend/WebContent/WEB-INF/lib/guava-17.0.jar
diff --git a/backend/lib/hamcrest-core-1.3.jar b/backend/WebContent/WEB-INF/lib/hamcrest-core-1.3.jar
similarity index 100%
rename from backend/lib/hamcrest-core-1.3.jar
rename to backend/WebContent/WEB-INF/lib/hamcrest-core-1.3.jar
diff --git a/backend/lib/httpclient-4.5.1.jar b/backend/WebContent/WEB-INF/lib/httpclient-4.5.1.jar
similarity index 100%
rename from backend/lib/httpclient-4.5.1.jar
rename to backend/WebContent/WEB-INF/lib/httpclient-4.5.1.jar
diff --git a/backend/lib/httpclient-4.5.3.jar b/backend/WebContent/WEB-INF/lib/httpclient-4.5.3.jar
similarity index 100%
rename from backend/lib/httpclient-4.5.3.jar
rename to backend/WebContent/WEB-INF/lib/httpclient-4.5.3.jar
diff --git a/backend/lib/httpcore-4.4.3.jar b/backend/WebContent/WEB-INF/lib/httpcore-4.4.3.jar
similarity index 100%
rename from backend/lib/httpcore-4.4.3.jar
rename to backend/WebContent/WEB-INF/lib/httpcore-4.4.3.jar
diff --git a/backend/lib/httpcore-4.4.6.jar b/backend/WebContent/WEB-INF/lib/httpcore-4.4.6.jar
similarity index 100%
rename from backend/lib/httpcore-4.4.6.jar
rename to backend/WebContent/WEB-INF/lib/httpcore-4.4.6.jar
diff --git a/backend/lib/httpmime-4.5.4.jar b/backend/WebContent/WEB-INF/lib/httpmime-4.5.4.jar
similarity index 100%
rename from backend/lib/httpmime-4.5.4.jar
rename to backend/WebContent/WEB-INF/lib/httpmime-4.5.4.jar
diff --git a/backend/lib/javassist-3.12.1.GA.jar b/backend/WebContent/WEB-INF/lib/javassist-3.12.1.GA.jar
similarity index 100%
rename from backend/lib/javassist-3.12.1.GA.jar
rename to backend/WebContent/WEB-INF/lib/javassist-3.12.1.GA.jar
diff --git a/backend/lib/javax.json-1.0.2.jar b/backend/WebContent/WEB-INF/lib/javax.json-1.0.2.jar
similarity index 100%
rename from backend/lib/javax.json-1.0.2.jar
rename to backend/WebContent/WEB-INF/lib/javax.json-1.0.2.jar
diff --git a/backend/lib/jdom-1.1.jar b/backend/WebContent/WEB-INF/lib/jdom-1.1.jar
similarity index 100%
rename from backend/lib/jdom-1.1.jar
rename to backend/WebContent/WEB-INF/lib/jdom-1.1.jar
diff --git a/backend/lib/joda-time-2.9.9.jar b/backend/WebContent/WEB-INF/lib/joda-time-2.9.9.jar
similarity index 100%
rename from backend/lib/joda-time-2.9.9.jar
rename to backend/WebContent/WEB-INF/lib/joda-time-2.9.9.jar
diff --git a/backend/lib/json-simple-1.1.1.jar b/backend/WebContent/WEB-INF/lib/json-simple-1.1.1.jar
similarity index 100%
rename from backend/lib/json-simple-1.1.1.jar
rename to backend/WebContent/WEB-INF/lib/json-simple-1.1.1.jar
diff --git a/backend/lib/junit-4.12.jar b/backend/WebContent/WEB-INF/lib/junit-4.12.jar
similarity index 100%
rename from backend/lib/junit-4.12.jar
rename to backend/WebContent/WEB-INF/lib/junit-4.12.jar
diff --git a/backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar b/backend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar
similarity index 100%
rename from backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar
rename to backend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar
diff --git a/backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old b/backend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old
similarity index 100%
rename from backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old
rename to backend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old
diff --git a/backend/lib/mxPdf.jar b/backend/WebContent/WEB-INF/lib/mxPdf.jar
similarity index 100%
rename from backend/lib/mxPdf.jar
rename to backend/WebContent/WEB-INF/lib/mxPdf.jar
diff --git a/backend/lib/mxgraph-all.jar b/backend/WebContent/WEB-INF/lib/mxgraph-all.jar
similarity index 100%
rename from backend/lib/mxgraph-all.jar
rename to backend/WebContent/WEB-INF/lib/mxgraph-all.jar
diff --git a/backend/lib/stax-utils-20070216.jar b/backend/WebContent/WEB-INF/lib/stax-utils-20070216.jar
similarity index 100%
rename from backend/lib/stax-utils-20070216.jar
rename to backend/WebContent/WEB-INF/lib/stax-utils-20070216.jar
diff --git a/backend/lib/vecmath-1.5.2.jar b/backend/WebContent/WEB-INF/lib/vecmath-1.5.2.jar
similarity index 100%
rename from backend/lib/vecmath-1.5.2.jar
rename to backend/WebContent/WEB-INF/lib/vecmath-1.5.2.jar
diff --git a/backend/lib/xpp3-1.1.4c.jar b/backend/WebContent/WEB-INF/lib/xpp3-1.1.4c.jar
similarity index 100%
rename from backend/lib/xpp3-1.1.4c.jar
rename to backend/WebContent/WEB-INF/lib/xpp3-1.1.4c.jar
diff --git a/backend/web.xml b/backend/WebContent/WEB-INF/web.xml
similarity index 100%
rename from backend/web.xml
rename to backend/WebContent/WEB-INF/web.xml