[meta,cmake] Restructure project and introduce CMake tooling

Rearrange project to conform to current best-practices in modern C++ repo organization.

Introduce initial configuration file for the CMake meta-build system, based on the restructured organization.

scripts/runFileTest.sh

 #!/bin/bash
+
+function scdaq_test {
+    echo "Starting scdaq test with GMT P5 capture file: check for crash"
+    timeout 10s build/scdaq --config test/config/scdaq-gmt.conf | uniq -uc
+    GMTRET="${PIPESTATUS[0]}"
+    echo "#############################################################################"
+    echo "Starting scdaq test with CALO P5 capture file: check for crash"
+    timeout 10s build/scdaq --config test/config/scdaq-calo.conf | uniq -uc
+    CALORET="${PIPESTATUS[0]}"
+    echo "#############################################################################"
+    echo "Starting scdaq test with 2 passthrough P5 capture files: check for crash"
+    timeout 10s build/scdaq --config test/config/scdaq-passthrough.conf --nstreams 2 | uniq
+    MULTI_PIPELINE_RET="${PIPESTATUS[0]}"
+    if [[ "$GMTRET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
+        echo "SCDAQ test for GMT failed with exit code ${GMTRET}!"
+        GMT_FAILED=true
+    elif [ $(find test/data -name "*scout_GMT*" | wc -l) -eq 0 ] && [ $OUTPUT_EXPECTED = "true" ]; then
+        echo "SCDAQ test for GMT failed, no output files found!"
+        GMT_FAILED=true
+    fi
+    if [[ "$CALORET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
+        echo "SCDAQ test for CALO failed with exit code ${CALORET}!"
+        CALO_FAILED=true
+    elif [ $(find test/data -name "*scout_CALO*" | wc -l) -eq 0 ] && [ $OUTPUT_EXPECTED  = "true" ]; then
+        echo "SCDAQ test for CALO failed, no output files found!"
+        CALO_FAILED=true
+    fi
+    if [[ "$MULTI_PIPELINE_RET" -ne 124 ]]; then
+        echo "SCDAQ test for MULTIPLE PIPELINES failed with exit code ${MULTI_PIPELINE_RET}!"
+        MULTI_PIPELINE_FAILED=true
+    elif [[ $(find test/data -name "*scout_PASS1_CALO*" | wc -l) -eq 0 || $(find test/data -name "*scout_PASS2_GMT*" | wc -l) -eq 0 ]]; then
+        echo "SCDAQ test for MULTIPLE PIPELINES failed, no output files found!"
+        MULTI_PIPELINE_FAILED=true
+    fi
+}
+
 echo "building scdaq locally"
 mkdir -p build
 cd build
@@ -8,29 +44,31 @@ cd ../test/data
 tar -xzvf calo_testfile.tar.gz
 tar -xzvf gmt_testfile.tar.gz
 cd ../../
-echo "Starting scdaq test with GMT P5 capture file: check for crash"
-timeout 20s build/scdaq --config test/config/scdaq-gmt.conf | uniq
-GMTRET="${PIPESTATUS[0]}"
-echo "#############################################################################"
-echo "Starting scdaq test with CALO P5 capture file: check for crash"
-timeout 60s build/scdaq --config test/config/scdaq-calo.conf | uniq
-CALORET="${PIPESTATUS[0]}"
-if [[ "$GMTRET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
-    echo "SCDAQ test for GMT failed with exit code ${GMTRET}!"
-    GMT_FAILED=true
-elif [[ $(find test/data -name "*scout_GMT*" | wc -l) -eq 0 ]]; then
-    echo "SCDAQ test for GMT failed, no output files found!"
-    GMT_FAILED=true
-fi
-if [[ "$CALORET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
-    echo "SCDAQ test for CALO failed with exit code ${CALORET}!"
-    CALO_FAILED=true
-elif [[ $(find test/data -name "*scout_CALO*" | wc -l) -eq 0 ]]; then
-    echo "SCDAQ test for CALO failed, no output files found!"
-    CALO_FAILED=true
-fi
+OUTPUT_EXPECTED=false
+scdaq_test
+echo $GMT_FAILED
+echo $CALO_FAILED
+echo $MULTI_PIPELINE_FAILED
+
+echo "Starting second set of test files"
+OUTPUT_EXPECTED=true
+cd test/data
+rm calo_testfile.dat
+rm gmt_testfile.dat
+tar -xzvf calo_testfile_mod.tar.gz
+tar -xzvf gmt_testfile_mod.tar.gz
+rm -rf run000000/in_progress/*
+cd ../../
+#next line needed because older GMT files were taken with 5 orbits per packet
+sed -i 's/nOrbitsPerPacket:1/nOrbitsPerPacket:5/' test/config/scdaq-gmt.conf
+scdaq_test
+
+echo $GMT_FAILED
+echo $CALO_FAILED
+echo $MULTI_PIPELINE_FAILED
+
 
-if [[ $GMT_FAILED = true || $CALO_FAILED = true ]]; then
+if [[ $GMT_FAILED = true || $CALO_FAILED = true || $MULTI_PIPELINE_FAILED = true ]]; then
     exit 1
 fi