README Clarifications and Fixup

* Clarified usage of gdb in README
* Addition of connect.sh script to help with gdb
* Fixup to move copying of kern directory to os161-1.99 directory to the
build_kernel function rather than unpack.
* Added git to the container

.gitignore

 assignments
+logs

README.md

@@ -49,16 +49,43 @@ assignment number.
 
 Within the container you may run within the shell (these functions are preloaded in your shell):
 ```
-build_kernel ASST0
-test_kernel ASST0
+# build_kernel ASST0
+# test_kernel ASST0
 ```
 To build and run within the context of ASST0. Finally you may evaluate your assignment based off public test cases (there could be hidden ones not found within
 the repo)
 
 ```
-/evalaute /logs/test_public.log /assignments/ASST0
+# /evalaute /logs/test_public.log /assignments/ASST0
 ```
 
+## Running GDB
+
+To run GDB, in a window with the container running and having built the kernel using the `build_kernel ASST0`:
+```
+# cd /os-compile/
+# sys161 -w kernel
+```
+
+Now in another terminal, move to this project directory and use the `./connect.sh` script to connect to the running container:
+```
+# cd /os-compile/
+# cs350-gdb kernel
+# cd os-compile/
+# cs350-gdb kernel
+
+GNU gdb 6.6
+Copyright (C) 2006 Free Software Foundation, Inc.
+...
+(gdb) dir /kernel/kern/compile/ASST0
+...
+```
+You will need to use the command `dir /kernel/kern/compile/ASST#` where `#` is the assignment number. This will make sure to load the symbols
+of the kernel. Symbols are the names we have given functions and variables, this allows gdb to convey what you are looking at (this is because
+the kernel has been compiled WITH these symbols in mind), otherwise gdb will show just bare assembly!
+
+Note: If `./connect.sh` does not work it may be because you have multiple running containers of os161-runner. Use `docker ps` to figure this out.
+This script is not a smart script just an ease of use script.
 
 ## Running other assignments
 You may point the `run.sh` to any directory as all this does is makes sure that the directory is shared between the container and you. Allowing you to
@@ -72,6 +99,7 @@ When mounting other directories that are not os161 note that the `build_kernel`
 There are some noted directories within the container
 * `/kernel` holds YOUR assignment code
 * `/os161-1.99` holds unchanged os161 kernel code
+* `/os-compile` holds the compiled version of the code
 * `/assignments` holds testing and evaluation scripts used for each assignment
 
 Within the `/assignments` directory there are subdirectories for each assignment, to see the test cases we pass and use, looks to the `public` file,

connect.sh

+#/usr/bin/env bash
+ID=`docker ps -aqf "ancestor=os161-runner"`
+docker exec -it $ID /bin/bash

os161-container/Dockerfile

 FROM ubuntu:18.04
 
-
 # Update gcc - ubuntu is used cause seems alpine gets upset
 RUN apt-get update && \
-    apt-get install --no-install-recommends -y gcc make wget g++ python3 libncurses-dev python3-pip && \
+    apt-get install --no-install-recommends -y gcc make wget g++ python3 libncurses-dev python3-pip git && \
     rm -rf /var/lib/apt/lists/*
 
 # Setup directories

os161-container/helpers.sh

@@ -6,12 +6,12 @@ export PATH=$PATH:/os161/tools/bin
 unpack_kernel() {
 	mkdir /kernel 
 	tar -xf /assignment.tgz -C /kernel --strip-components 1
-	cp -r /kernel/kern/* $OS161_DIR/kern/
 }
 
 build_k_helper() {
 	cd $OS161_DIR
 	mkdir /os-compile
+	cp -r /kernel/kern/* $OS161_DIR/kern/
 	set -e
 	# Configure - step 1
 	echo "[CS350] $1 Configuring Kernel..."