update docs/helpers for unified format

Author: rshariffdeen

README.md

@@ -92,6 +92,30 @@ The backported patch to target version PC is as follows:
     >       if (author_list[b].user_id < minimum) {
     >         minimum = author_list[b].user_id;
 ```
+If you prefer changes to display in unified diff format, use the additional flag
+"--format=unified" 
+
+```c
+--- /FixMorph/tests/update/assignment/PC/selection-sort.c	
++++ /FixMorph/tests/update/assignment/PC-patch/selection-sort.c	
+
+@@ -15,11 +15,11 @@
+while (a < length) {
+    author_id = author_list[a].user_id;
+    rank = author_list[a].rank;
+    -    minimum = rank;
+    +    minimum = author_id;
+    position = a;
+    for (b = a + 1; b < length; b++) {
+    -      if (author_list[b].rank < minimum) {
+    -        minimum = author_list[b].rank;
+    +      if (author_list[b].user_id < minimum) {
+    +        minimum = author_list[b].user_id;
+    position = b;
+    }
+}
+```
+
 Many such examples are included in the 'tests' directory, simply replace the configuration file path and run the same command as above.
 
 # Limitations #

app/tools/emitter.py

@@ -187,6 +187,7 @@ def help():
     print("\t" + definitions.ARG_TIMEOUT + "\t| " + "timeout in minutes (default=60)")
     print("\t" + definitions.ARG_OPERATION_MODE + "\t| " + "select which tool/mode to run for backport {0: fixmorph, 1: patch, 2: patch-context, 3: sydit}")
     print("\t" + definitions.ARG_CONTEXT_LEVEL + "\t| " + "set context level for patch-context mode")
+    print("\t" + definitions.ARG_OUTPUT_FORMAT + "\t| " + "select the output format for the diff change {'normal', 'unified'} (default = normal)")
 
     print("Skip Phases\n-----------------------\n")
     print("\t" + definitions.ARG_SKIP_BUILD + "\t| " + "skip build")

app/tools/weaver.py

@@ -121,7 +121,7 @@ def show_patch(file_a, file_b, file_c, file_d, index):
     emitter.highlight("\tOriginal Patch")
     original_patch_file_name = definitions.DIRECTORY_OUTPUT + "/" + index + "-original-patch"
     generated_patch_file_name = definitions.DIRECTORY_OUTPUT + "/" + index + "-generated-patch"
-    diff_command = "diff -ENZBbwr"
+    diff_command = "diff -ENZBbwr "
     if values.DEFAULT_OUTPUT_FORMAT == "unified":
         diff_command += " -u "
     diff_command += file_a + " " + file_b + " > " + original_patch_file_name
@@ -133,7 +133,7 @@ def show_patch(file_a, file_b, file_c, file_d, index):
             diff_line = diff.readline().strip()
 
     emitter.highlight("\tGenerated Patch")
-    diff_command = "diff -ENZBbwr"
+    diff_command = "diff -ENZBbwr "
     if values.DEFAULT_OUTPUT_FORMAT == "unified":
         diff_command += " -u "
     diff_command += file_c + " " + file_d + " > " + generated_patch_file_name

doc/Manual.md

@@ -30,7 +30,8 @@ The tool supports the following runtime configurations:
 		--debug	            | enable debugging information
 		--mode=             | execution mode [0: fixmorph 1: linux-patch-no-context 2: linux-patch-context 3: sydit] (default = 0)
 		--context=          | context level for linux-patch-context mode
-
+ 		--format=           | select format for diff changes [normal, unified] (default=normal)
+ 
 
 ### Side effects ###
 

experiments/ISSTA21/README.md

@@ -40,6 +40,7 @@ docker pull rshariffdeen/fixmorph:issta21
 ```
 
 Having the image, you can now start a Docker container. 
+Note: please make sure to use the correct image which has the dependencies installed for Linux kernel (i.e. rshariffdeen/fixmorph:issta21)
 
 [comment]: <> (We recommend linking the container to folders in the filesystem,)
 [comment]: <> (so that it is possible to check the logs and generated outputs also outside of the Docker container. )