updating readme

Author: harsha-simhadri

README_PROTONN_OSS.md

@@ -114,12 +114,14 @@ Most users should copy this section directly to all their ProtoNN execution scri
 - **Errors and warnings** are printed to **std::cerr**. 
 
 - Additional **parameter dumps**, **timer logs** and other **debugging logs** will be placed in the input folder `foo`. Hence, the user should have read-write permissions on `foo` (use chmod if necessary). 
-    -  On execution, a folder called `ProtoNNResults` is created in `foo`. The results folder will have another folder whose name will indicate to the user the list of parameters with which the run was instantiated. In this folder, upto **6 files** will be created depending on which flags are set in `config.mk`: 
-    - **diagnosticLog**: Created on using the `LOGGER` or `LIGHT_LOGGER` flags. This file stores logging information such as the call flow of ProtoNN and the min, max, norms of various matrices. This is mainly for debugging/optimization purposes and requires a more detailed understanding of the code to interpret. It may contain useful information if your code did not run as expected. **The log file is populated synchronously while the ProtoNN optimization is executing.** 
-    - **timerLog**: Created on using the `TIMER` flag. This file stores proc time and wall time taken to execute various function calls in the code. Indicates the degree of parallelization and is useful for identifying bottlenecks to optimize the code. On specifying the `CONCISE` flag, timing information will only be printed if running time is higher than a threshold specified in `src/common/timer.cpp`.
+    -  On execution, a folder called `ProtoNNResults` is created in `foo`. The results folder will have another folder whose name will indicate to the user the list of parameters with which the run was instantiated. In this folder, upto **6 files** and **2 folders** will be created depending on which flags are set in `config.mk`: 
     - **runInfo**: This file contains the hyperparameters and meta-information for the respective instantiation of ProtoNN. It also shows you the exact bash script call that was made, which is helpful for reproducing results purposes. Additionally, the training, testing accuracy and objective value at the end of each iteration is printed in a readable format. **This file is created at the end of the ProtoNN optimization.**
     - **W, B, Z**: These files contain the learnt parameter matrices $$W$$, $$B$$ and $$Z$$ in human-readable tsv format. The dimensions of storage are $$(d, D)$$, $$(d, m)$$ and $$(L, m)$$ respectively. **These files are created at the end of the ProtoNN optimization.**
-    - **gamma**: This file contains a single number, the chosen value of $$\gamma$$, the RBF kernel parameter.
+    - **gamma**: This file contains a single number, the chosen value of $$\gamma$$, the RBF kernel parameter. **This file is created at the end of the ProtoNN optimization.**
+    - **diagnosticLog**: Created on using the `LOGGER` or `LIGHT_LOGGER` flags. This file stores logging information such as the call flow of ProtoNN and the min, max, norms of various matrices. This is mainly for debugging/optimization purposes and requires a more detailed understanding of the code to interpret. It may contain useful information if your code did not run as expected. **The diagnosticLog file is populated synchronously while the ProtoNN optimization is executing.** 
+    - **timerLog**: Created on using the `TIMER` flag. This file stores proc time and wall time taken to execute various function calls in the code. Indicates the degree of parallelization and is useful for identifying bottlenecks to optimize the code. On specifying the `CONCISE` flag, timing information will only be printed if running time is higher than a threshold specified in `src/common/timer.cpp`. **The timerLog file is populated synchronously while the ProtoNN optimization is executing.**  
+    - **dump**: A folder that is created on using the `DUMP` flag. The parameter matrices are outputted after each iteration in this folder. **This folder is populated synchronously while the ProtoNN optimization is executing.**
+    - **verify**: A folder that is created on using the `VERIFY` flag. Code for backward verification with legacy Matlab code. **This folder is populated synchronously while the ProtoNN optimization is executing.**
 
 The files **W, B, Z**, and **gamma** can be copied to `foo` to continue training of ProtoNN by initializing with these previously learned matrices. Use the **-P** option for this (see above). On doing so, the starting train/test accuracies should match the final accuracy as specified in the runInfo file.