1) Make ProvisionData, DATABASE and PROTOCOL directories in the directory where you created lab2 and HOST2023 (called the BASE directory)
mkdir ProvisionData
mkdir DATABASE

Your directory structure should look like
lab2
HOST2023
ProvisionData
DATABASE
PROTOCOL

NOTE: DO NOT DO YOUR LABS in the github directory, HOST2023

2) cd into DATABASE
cd DATABASE

3) Copy all the files in the DATABASE directory on the website here. NOTE: There is a SQLSchemaScripts subdirectory!
# (whatever copy method you use)

4) Make an output directory
mkdir output

5) Change back to BASE directory.
cd ..

6) cd into PROTOCOL
cd PROTOCOL

7) Copy all the files in the PROTOCOL directory on the website to your PROTOCOL directory (whatever copy method you use)
8) cd into ProvisionData and copy the files from the HOST2023 repository here
cd ../ProvisionData
cp -p ../HOST2023/ProvisionData/* .

9) Change to DATABASE
../DATABASE

10) Compile the programs.
make -f Makefile_AddChallengeDB
make -f Makefile_EnrollDB
make -f Makefile_add_PUFDesign_challengeDB

11) Create NAT_Master_TDC.db (non-anonymous timing database) (Note: You must have sqlite3 installed) 
NOTE: If you need to start over with the database creation process, start by removing the databases (rm *.db) and re-running these scripts
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_PUFDesign_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_PUFInstance_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_VecPairs_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_Vectors_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_TimingVals_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_PathSelectMasks_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_Challenges_create_table.sql
sqlite3 NAT_Master_TDC.db < SQLSchemaScripts/SQL_ChallengeVecPairs_create_table.sql

sqlite3 Challenges.db < SQLSchemaScripts/SQL_PUFDesign_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_PUFInstance_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_VecPairs_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_Vectors_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_TimingVals_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_PathSelectMasks_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_Challenges_create_table.sql
sqlite3 Challenges.db < SQLSchemaScripts/SQL_ChallengeVecPairs_create_table.sql

12) Add the provisioning data to the database
NOTE: You will eventually need to ADD ALL Provisioning data to the database, i.e., ALL files in the HOST2023/ProvisionData directory. Do `git pull' as needed and do the cp command above to copy the files from the HOST2023 repository to your local ../ProvisionData directory.
NOTE: If you want to do your files first, change the 'C_Jim_204' to your filename prefix
NOTE: ALWAYS USE ZYBO, even if you have a CORA board in the following!
NOTE: CHECK output/enrollDB... file for errors.
NOTE: Add additional `enrollDB' command lines for the other files in the ProvisionData directory.

My CORA files:
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P1 Z_Jim_64 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/Z_Jim_64_SR_RFM_V4_TDC_P1_25C_1.00V_NCs_2000_E_PUFNums.txt > output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P2 Z_Jim_64 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/Z_Jim_64_SR_RFM_V4_TDC_P2_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P3 Z_Jim_64 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/Z_Jim_64_SR_RFM_V4_TDC_P3_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P4 Z_Jim_64 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/Z_Jim_64_SR_RFM_V4_TDC_P4_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt

My ZYBO files
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P1 C_Jim_204 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/C_Jim_204_SR_RFM_V4_TDC_P1_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P2 C_Jim_204 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/C_Jim_204_SR_RFM_V4_TDC_P2_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P3 C_Jim_204 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/C_Jim_204_SR_RFM_V4_TDC_P3_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt
   enrollDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 ZYBO P4 C_Jim_204 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 ../ProvisionData/C_Jim_204_SR_RFM_V4_TDC_P4_25C_1.00V_NCs_2000_E_PUFNums.txt >> output/enrollDB_SR_RFM_V4_TDC_SRFSyn1_Cx_Vx.txt

13) Add challenge to NAT_Master_TDC.db
add_challengeDB NAT_Master_TDC.db SR_RFM_V4_TDC SRFSyn1 Master1_OptKEK_TVN_0.00_WID_1.75 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10 ../CHALLENGES/optKEK_qualifing_path_TVN_0.00_WID_1.75_SetSize_64000 1 > output/add_challengeDB_SRFSyn1_Master1_OptKEK_TVN_0.00_WID_1.75.txt

14) Make a copy of the NAT_Master_TDC.db to AT_Master_TDC.db (anonymous timing database)
cp NAT_Master_TDC.db AT_Master_TDC.db

15) Add challenges to Challenges.db
add_PUFDesign_challengeDB Challenges.db SR_RFM_V4_TDC SRFSyn1 CORA P1 Cxx 392 32 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10_vecs 0 > output/add_challengeDB_SRFSyn1_Master1_OptKEK_TVN_0.00_WID_1.75_Challenges.txt
add_challengeDB Challenges.db SR_RFM_V4_TDC SRFSyn1 Master1_OptKEK_TVN_0.00_WID_1.75 ../CHALLENGES/SR_RFM_V4_Random_Rise_1000Vs_Fall_1000Vs_NumSeeds_10 ../CHALLENGES/optKEK_qualifing_path_TVN_0.00_WID_1.75_SetSize_64000 0 > output/add_challengeDB_SRFSyn1_Master1_OptKEK_TVN_0.00_WID_1.75_Challenges.txt