Restructure the instructions according to the figure

code/README.md

@@ -34,19 +34,24 @@ To fetch issues from Jenkins JIRA, just run:
 ```python
 python fetch.py
 ```
-It creates a directory with issues (see issues folder in the [figure](#workflow)). These issues will later on be used by the `find_bug_fixes.py` script. Second we need to convert the `git log` output to something that can be processed. That requires a local copy of the repository that we aim to analyze, [Jenkins Core Repository](https://github.com/jenkinsci/jenkins). Onced cloned, one can now run the **git_log_to_array.py** script (see 2) in the [figure](#workflow)). The script requires an absolute path to the cloned repository and optionally a SHA-1 for an initial commit.
+It creates a directory with issues (see issues folder in the [figure](#workflow)). These issues will later on be used by the `find_bug_fixes.py` script. 
+
+### Step 2. Preprocess the git log output (SZZ pre-step) ###
+Second we need to convert the `git log` output to something that can be processed. That requires a local copy of the repository that we aim to analyze, [Jenkins Core Repository](https://github.com/jenkinsci/jenkins). Onced cloned, one can now run the **git_log_to_array.py** script (see 2) in the [figure](#workflow)). The script requires an absolute path to the cloned repository and optionally a SHA-1 for an initial commit.
 ```python
 python git_log_to_array.py --repo-path <path_to_local_repo>
 ```
-Once executed, this creates a file `gitlog.json` that can be used together with issues that we created with `fetch.py` script. Now using the `find_bug_fixes.py` (see 3) in the [figure](#workflow)) and this file, we can get a json file
+Once executed, this creates a file `gitlog.json` that can be used together with issues that we created with `fetch.py` script. 
+
+### Step 3. Identify bug-fixing commits (SZZ Phase 1) ###
+Now using the `find_bug_fixes.py` (see 3) in the [figure](#workflow)) and this file, we can get a json file
 that contains the Issue and its corresponding commit SHA-1, the commit date, the creation date and the resolution date. Just run:
 ```python
 python find_bug_fixes.py --gitlog <path_to_gitlog_file> --issue-list <path_to_issues_directory>
 ```
 The output is `issue_list.json` which is later used in the SZZ algorithm.
 
-### Find the bug-introducing commits ###
-
+### Identify bug-introducing commits (SZZ Phase 2) ###
 This implementation works regardless which language and file type. It uses
 [JGIT](https://www.eclipse.org/jgit/) to parse a git repository.
 
@@ -72,8 +77,7 @@ by the previous issue to bug fix commit step, run (see 4) in the [figure](#workf
 java -jar szz_find_bug_introducers-<version_number>.jar -i <path_to_issue_list.json> -r <path_to_local_repo>
 ```
 
-## Output
-
+## Output from SZZ Unleashed
 As shown in the [figure](#workflow), the output consists of three different files: commits.json,
 annotations.json and fix\_and\_bug\_introducing\_pairs.json.