Fix: remove 29 orphaned #+end_src tags leaking as visible text

When a markdown code block demonstrated org #+end_src syntax, the
md→org converter consumed that #+end_src as the block's closing tag,
leaving the real closing tag as a stray #+end_src outside any block.
fix_org_blocks.py then made things worse by leaving it unmatched.

Affected: ch03 (1), ch11 (24), ch12 (1), ch13 (3).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: DavidLiedle

03-document-structure.org

@@ -240,7 +240,6 @@ def fibonacci(n):
         return n
     return fibonacci(n-1) + fibonacci(n-2)
 #+end_example
-#+end_src
 
 We'll dive deep into code blocks in Chapter 11 (spoiler: they're executable).
 

11-code-blocks-literate-programming.org

@@ -18,7 +18,6 @@ We've seen this syntax:
 def hello():
     print("Hello from Org-Mode!")
 #+end_example
-#+end_src
 
 But here's the magic. Put cursor in the block and press =C-c C-c=:
 
@@ -97,7 +96,6 @@ print("Line 1")
 print("Line 2")
 print("Line 3")
 #+end_example
-#+end_src
 
 Execute with =C-c C-c=:
 
@@ -147,7 +145,6 @@ x = 42
 #+BEGIN_SRC python
 print(x)  # Error: x not defined
 #+END_SRC
-#+end_src
 
 With sessions, state persists:
 
@@ -159,7 +156,6 @@ x = 42
 #+BEGIN_SRC python :session
 print(x)  # Works! Outputs: 42
 #+END_SRC
-#+end_src
 
 Same Python interpreter, same namespace. Variables, functions, imports—all persist.
 
@@ -173,7 +169,6 @@ x = 1
 #+BEGIN_SRC python :session project-b
 x = 2
 #+END_SRC
-#+end_src
 
 Separate environments, same document.
 
@@ -188,7 +183,6 @@ print(f"{name} is {age} years old")
 
 #+RESULTS:
 : Alice is 30 years old
-#+end_src
 
 ** Variables from Tables
 
@@ -210,7 +204,6 @@ print(df.sum(numeric_only=True))
 : Q2    40
 : Q3    42
 : Q4    46
-#+end_src
 
 Table becomes 2D list. Process with any language.
 
@@ -228,7 +221,6 @@ print(sum(numbers))
 
 #+RESULTS:
 : 15
-#+end_src
 
 Chain blocks together. One block's output feeds another's input.
 
@@ -252,7 +244,6 @@ return [
 | Alice |  28 | Portland  |
 | Bob   |  35 | Seattle   |
 | Carol |  42 | Vancouver |
-#+end_src
 
 Generate org tables from code. Add formulas. Instant data reports.
 
@@ -276,7 +267,6 @@ return 'sine.png'
 
 #+RESULTS:
 [[file:sine.png]]
-#+end_src
 
 The plot appears in your document. Update code, re-execute, plot updates.
 
@@ -286,7 +276,6 @@ With R:
 #+BEGIN_SRC R :results graphics file :file plot.png
 plot(cars)
 #+end_example
-#+end_src
 
 With gnuplot, ditaa, graphviz—dozens of options.
 
@@ -351,7 +340,6 @@ print(f"Recursive: {result1} in {time1:.4f}s")
 print(f"Iterative: {result2} in {time2:.6f}s")
 print(f"Speedup: {time1/time2:.0f}x")
 #+END_SRC
-#+end_src
 
 Code, explanation, tests, benchmarks—all in one document. Export to PDF for sharing, execute for verification.
 
@@ -373,7 +361,6 @@ def fibonacci(n):
 if __name__ == "__main__":
     print([fibonacci(i) for i in range(10)])
 #+end_example
-#+end_src
 
 Run =M-x org-babel-tangle= or =C-c C-v t=. Org extracts code to =fib.py=.
 
@@ -395,7 +382,6 @@ def main():
 if __name__ == "__main__":
     main()
 #+END_SRC
-#+end_src
 
 Tangle creates =program.py= with all blocks combined in order.
 
@@ -427,7 +413,6 @@ def main():
 if __name__ == "__main__":
     main()
 #+END_SRC
-#+end_src
 
 =<<blockname>>= inserts that block's content. Compose programs from pieces.
 
@@ -458,7 +443,6 @@ SELECT name, age FROM users WHERE age > 25;
 | Alice |  28 |
 | Bob   |  35 |
 | Carol |  42 |
-#+end_src
 
 Results as org tables. Add formulas, analyze data.
 
@@ -468,7 +452,6 @@ With PostgreSQL:
 #+BEGIN_SRC sql :engine postgresql :database mydb :user myuser
 SELECT * FROM orders WHERE status = 'pending';
 #+end_example
-#+end_src
 
 Your documentation queries production databases. Be careful, but powerful.
 
@@ -485,7 +468,6 @@ ls -la ~/org | head -10
 : drwxr-xr-x+  87 user  staff  2784 Jan 15 09:15 ..
 : -rw-r--r--    1 user  staff  2048 Jan 14 15:20 inbox.org
 : ...
-#+end_src
 
 Document system administration with executable examples.
 
@@ -496,14 +478,12 @@ Document system administration with executable examples.
 #+BEGIN_SRC shell :dir ~/projects/myapp
 ls
 #+end_example
-#+end_src
 
 *:file* - Output file:
 #+begin_example
 #+BEGIN_SRC dot :file diagram.png
 digraph { A -> B; B -> C; }
 #+end_example
-#+end_src
 
 *:cache* - Cache results:
 #+begin_example
@@ -513,7 +493,6 @@ import time
 time.sleep(5)
 return "Done"
 #+end_example
-#+end_src
 
 Re-run only if code changes.
 
@@ -522,15 +501,13 @@ Re-run only if code changes.
 #+BEGIN_SRC shell :cmdline -n 5
 head
 #+end_example
-#+end_src
 
 *:stdin* - Provide input:
 #+begin_example
 #+BEGIN_SRC python :stdin example-data
 import sys
 print(sys.stdin.read().upper())
 #+end_example
-#+end_src
 
 * Document-Wide Defaults
 
@@ -554,7 +531,6 @@ Per-subtree:
 #+BEGIN_SRC python
 print("Uses :session py :results output")
 #+end_example
-#+end_src
 
 * Reproducible Research
 

12-export-publishing.org

@@ -330,7 +330,6 @@ Remember =:exports= from Chapter 11?
 #+BEGIN_SRC python :exports both
 print("Hello!")
 #+end_example
-#+end_src
 
 - =:exports code= - Show only code in export
 - =:exports results= - Show only output

13-advanced-features.org

@@ -154,7 +154,6 @@ Execute code on remote machines:
 #+BEGIN_SRC shell :dir /ssh:user@remote:/path/to/dir
 ls -la
 #+end_example
-#+end_src
 
 Tramp integration. Document remote operations.
 
@@ -176,7 +175,6 @@ return [[item['name'], item['value']] for item in parsed['items']]
 #+BEGIN_SRC R :var dataset=previous-block
 plot(dataset)
 #+END_SRC
-#+end_src
 
 Fetch with shell → Parse with Python → Visualize with R. All in one document.
 
@@ -199,7 +197,6 @@ assert calculate_tax(0) == 0
 assert calculate_tax(50) == 10
 print("All tests passed!")
 #+END_SRC
-#+end_src
 
 Tests live with documentation. Update function → re-run tests.