Fix \split conflict, add .gitignore for build artifacts

- Renamed \split → \splitnote (\split already defined by another package)
- Added .gitignore for *.aux, *.log, *.pdf, etc.
- Branch switching now clean — just recompile after switch

.gitignore

@@ -0,0 +1,38 @@
+# LaTeX build artifacts
+*.aux
+*.bbl
+*.blg
+*.fdb_latexmk
+*.fls
+*.log
+*.out
+*.synctex.gz
+*.toc
+*.lof
+*.lot
+*.nav
+*.snm
+*.vrb
+*.dvi
+*.ps
+
+# Generated PDF (recompile from source)
+main.pdf
+
+# Todonotes list
+*.tdo
+
+# Backup files
+*.bak
+*~
+\#*\#
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Editor files
+*.swp
+*.swo
+.vscode/
+.idea/

1-goals-and-outcomes/goals.tex

@@ -3,7 +3,7 @@
 % GOAL PARAGRAPH
 The goal of this research is to develop a methodology for creating autonomous
 hybrid control systems with mathematical guarantees of safe and correct
-behavior.\split{Strong opening — direct and clear. No changes needed.}
+behavior.\splitnote{Strong opening — direct and clear. No changes needed.}
 
 % INTRODUCTORY PARAGRAPH Hook
 Nuclear power plants require the highest levels of control system reliability,
@@ -17,14 +17,14 @@ switch between different control modes based on their interpretation of plant
 conditions and procedural guidance.
 % Gap
 This reliance on human operators prevents autonomous control capabilities and
-creates a fundamental economic challenge for next-generation reactor designs.\split{Consider: ``...and creates a fundamental economic challenge'' — the ``and'' makes this feel like two separate issues. Maybe split into two sentences or tighten the causal link?}
+creates a fundamental economic challenge for next-generation reactor designs.\splitnote{Consider: ``...and creates a fundamental economic challenge'' — the ``and'' makes this feel like two separate issues. Maybe split into two sentences or tighten the causal link?}
 Small modular reactors, in particular, face per-megawatt staffing costs far
 exceeding those of conventional plants and threaten their economic viability.
 
 % Critical Need
 What is needed is a method to create autonomous control systems that safely
 manage complex operational sequences with the same assurance as human-operated
-systems, but without constant human supervision.\split{``What is needed is'' — classic Gopen weak opening. Try: ``Autonomous control systems must safely manage...'' — puts the subject in the topic position.}
+systems, but without constant human supervision.\splitnote{``What is needed is'' — classic Gopen weak opening. Try: ``Autonomous control systems must safely manage...'' — puts the subject in the topic position.}
 % APPROACH PARAGRAPH Solution
 To address this need, we will combine formal methods with control theory to
 build hybrid control systems that are correct by construction.

main.aux

@@ -1,8 +1,20 @@
 \relax 
 \@writefile{toc}{\contentsline {section}{Contents}{ii}{}\protected@file@percent }
 \@writefile{toc}{\contentsline {section}{\numberline {1}Goals and Outcomes}{1}{}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{\fcolorbox {black}{green!40}{\textcolor {green!40}{o}}\ Strong opening — direct and clear. No changes needed.}{1}{}\protected@file@percent }
+\pgfsyspdfmark {pgfid1}{25927240}{44563390}
+\pgfsyspdfmark {pgfid4}{38491976}{44537654}
+\pgfsyspdfmark {pgfid5}{40806441}{44297970}
+\@writefile{tdo}{\contentsline {todo}{\fcolorbox {black}{green!40}{\textcolor {green!40}{o}}\ Consider: ``...and creates a fundamental economic challenge'' — the ``and'' makes this feel like two separate issues. Maybe split into two sentences or tighten the causal link?}{1}{}\protected@file@percent }
+\pgfsyspdfmark {pgfid6}{6549774}{36961214}
+\pgfsyspdfmark {pgfid9}{38491976}{36935478}
+\pgfsyspdfmark {pgfid10}{40806441}{36695794}
+\@writefile{tdo}{\contentsline {todo}{\fcolorbox {black}{green!40}{\textcolor {green!40}{o}}\ ``What is needed is'' — classic Gopen weak opening. Try: ``Autonomous control systems must safely manage...'' — puts the subject in the topic position.}{1}{}\protected@file@percent }
+\pgfsyspdfmark {pgfid11}{10907275}{33160126}
+\pgfsyspdfmark {pgfid14}{38491976}{21872198}
+\pgfsyspdfmark {pgfid15}{40806441}{21632514}
 \@writefile{tdo}{\contentsline {todo}{\fcolorbox {black}{green!40}{\textcolor {green!40}{o}}\ This qualifications paragraph feels a bit tacked-on here. Consider moving to the end of the Approach section or integrating it more naturally into the ``why it will succeed'' argument.}{1}{}\protected@file@percent }
-\pgfsyspdfmark {pgfid1}{20112834}{29690842}
+\pgfsyspdfmark {pgfid16}{20112834}{17337306}
 \citation{NUREG-0899,10CFR50.34}
 \citation{10CFR55.59}
 \citation{WRPS.Description,gentillon_westinghouse_1999}

main.blg

@@ -1,11 +1,11 @@
 This is BibTeX, Version 0.99d (TeX Live 2025)
 Capacity: max_strings=200000, hash_size=200000, hash_prime=170003
 The top-level auxiliary file: main.aux
-White space in argument---line 23 of file main.aux
+White space in argument---line 36 of file main.aux
  : \citation{HANDBOOK
  :                    ON HYBRID SYSTEMS}
 I'm skipping whatever remains of this command
-White space in argument---line 30 of file main.aux
+White space in argument---line 43 of file main.aux
  : \citation{MANYUS
  :                  THESIS}
 I'm skipping whatever remains of this command

main.fdb_latexmk

@@ -1,13 +1,13 @@
 # Fdb version 4
-["bibtex main"] 0 "main.aux" "main.bbl" "main" 1773106033.40961 -1
+["bibtex main"] 1773106474.93179 "main.aux" "main.bbl" "main" 1773106474.96468 2
   "./references.bib" 1770435796.31586 14069 2a4f74c587187a8a71049043171eb0fe ""
   "/Users/split/Library/TinyTeX/texmf-dist/bibtex/bst/base/ieeetr.bst" 1292289607 18361 1a00e58565e7f19bf2b3e1bfb82254ae ""
-  "main.aux" 1773106033.2376 6065 320072990cd0549d1222adda8966f923 "pdflatex"
+  "main.aux" 1773106474.76109 7231 2769f5164b2ddb0c968502f2788a9df8 "pdflatex"
   (generated)
   "main.bbl"
   "main.blg"
   (rewritten before read)
-["pdflatex"] 1773106032.05172 "main.tex" "main.pdf" "main" 1773106033.40982 2
+["pdflatex"] 1773106473.46494 "main.tex" "main.pdf" "main" 1773106474.96491 0
   "/Users/split/Library/TinyTeX/texmf-dist/fonts/enc/dvips/base/8r.enc" 1165713224 4850 80dc9bab7f31fb78a000ccfed0e27cab ""
   "/Users/split/Library/TinyTeX/texmf-dist/fonts/tfm/adobe/symbol/psyr.tfm" 1136768653 1408 5937f58aa508ea2cea4901c07d10f5fe ""
   "/Users/split/Library/TinyTeX/texmf-dist/fonts/tfm/adobe/times/psyro.tfm" 1136768653 1544 23a042a74981a3e4b6ce2e350e390409 ""
@@ -239,7 +239,7 @@
   "/Users/split/Library/TinyTeX/texmf-var/fonts/map/pdftex/updmap/pdftex.map" 1771879278 94137 fe53532163e1d92c794c09ef981daf8d ""
   "/Users/split/Library/TinyTeX/texmf-var/web2c/pdftex/pdflatex.fmt" 1770868900 2236375 139dae50424001d43c49d2d79a9c607f ""
   "/Users/split/Library/TinyTeX/texmf.cnf" 1770868853 637 edd806fb06a89761a6034e1968af9017 ""
-  "1-goals-and-outcomes/goals.tex" 1773106013.90511 6437 a0b91bc35049a7bdb682b56e09847db6 ""
+  "1-goals-and-outcomes/goals.tex" 1773106456.22497 6449 2997df4b13b90c69ee012b87ddd9cd94 ""
   "1-goals-and-outcomes/research-statement.tex" 1773105333.1977 4450 070caee751214eaddffa6b3403f8ed43 ""
   "2-state-of-the-art/state-of-art.tex" 1773105333.19841 12622 1460f7a4c2b48a1a772d8a0f5db216af ""
   "3-research-approach/approach.tex" 1773105333.19929 35753 93d4c7b608feeba783c33affa59dd220 ""
@@ -248,10 +248,10 @@
   "6-broader-impacts/impacts.tex" 1773105333.20065 4834 418aae223b778759691eaf9124a5360c ""
   "8-schedule/schedule.tex" 1773105333.20091 4473 8ad96bbf9cedf2ea09298ecbd4e01b83 ""
   "dane_proposal_format.cls" 1770435796.31147 2883 ea175794171aa0291ef71716b2190bf0 ""
-  "main.aux" 1773106033.2376 6065 320072990cd0549d1222adda8966f923 "pdflatex"
+  "main.aux" 1773106474.76109 7231 2769f5164b2ddb0c968502f2788a9df8 "pdflatex"
-  "main.bbl" 1773105333.20144 2919 0ea026a17b15c1ad2ed657bdbf26dfdc "bibtex main"
+  "main.bbl" 1773106474.96361 2919 0ea026a17b15c1ad2ed657bdbf26dfdc "bibtex main"
-  "main.tex" 1773106026.10519 1375 7713fbae9f240a12fde027387bdbcf87 ""
+  "main.tex" 1773106452.46565 1379 944a0991d85aa6b5966f2f945e5ef1a1 ""
-  "main.toc" 1773106033.2392 2129 eb658283ff0c872296846602d3e9dde6 "pdflatex"
+  "main.toc" 1773106474.76365 2129 eb658283ff0c872296846602d3e9dde6 "pdflatex"
   "todonotes.sty" 1773106013.90863 21404 916e19cbd009b6d289c8194b313d3895 ""
   (generated)
   "main.aux"

main.log

@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025) (preloaded format=pdflatex 2026.2.12)  9 MAR 2026 21:27
+This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025) (preloaded format=pdflatex 2026.2.12)  9 MAR 2026 21:34
 entering extended mode
  restricted \write18 enabled.
  %&-line parsing enabled.
@@ -774,20 +774,6 @@ Package: todonotes 2024/01/05 v1.1.7 Todonotes source and documentation.
 Package: todonotes 2024/01/05
 \c@@todonotes@numberoftodonotes=\count403
 )
-
-! LaTeX Error: Command \split already defined.
-               Or name \end... illegal, see p.192 of the manual.
-
-See the LaTeX manual or LaTeX Companion for explanation.
-Type  H <return>  for immediate help.
- ...                                              
-                                                  
-l.13 ...1]{\todo[color=green!40,author=Split]{#1}}
-                                                  
-Your command was ignored.
-Type  I <command> <return>  to replace it with another command,
-or  <return>  to continue without it.
-
 LaTeX Font Info:    Trying to load font information for OT1+ptm on input line 18.
  (/Users/split/Library/TinyTeX/texmf-dist/tex/latex/psnfss/ot1ptm.fd
 File: ot1ptm.fd 2001/06/04 font definitions for OT1/ptm.
@@ -899,40 +885,10 @@ LaTeX Font Info:    Font shape `OT1/ptm/bx/n' in size <7> not available
 \openout4 = `main.toc'.
 
  [2] (./1-goals-and-outcomes/goals.tex
-Runaway argument?
-\collect@body \gather@split {Strong opening — direct and clear. No \ETC.
-! Paragraph ended before \document was complete.
-<to be read again> 
-                   \par 
-l.7 
 
-I suspect you've forgotten a `}', causing me to apply this
+LaTeX Warning: Marginpar on page 1 moved.
-control sequence to too much text. How can we recover?
-My plan is to forget the whole thing and hope for the best.
 
-Runaway argument?
+[1]) [2] (./2-state-of-the-art/state-of-art.tex [3] [4] [5]) [6] (./3-research-approach/approach.tex
-\collect@body \gather@split {Consider: ``...and creates a fundamental\ETC.
-! Paragraph ended before \document was complete.
-<to be read again> 
-                   \par 
-l.23 
-     
-I suspect you've forgotten a `}', causing me to apply this
-control sequence to too much text. How can we recover?
-My plan is to forget the whole thing and hope for the best.
-
-Runaway argument?
-\collect@body \gather@split {``What is needed is'' — classic Gopen \ETC.
-! Paragraph ended before \document was complete.
-<to be read again> 
-                   \par 
-l.48 
-     
-I suspect you've forgotten a `}', causing me to apply this
-control sequence to too much text. How can we recover?
-My plan is to forget the whole thing and hope for the best.
-
-) [1] [2] (./2-state-of-the-art/state-of-art.tex [3] [4] [5]) [6] (./3-research-approach/approach.tex
 
 LaTeX Warning: Citation `HANDBOOK ON HYBRID SYSTEMS' on page 7 undefined on input line 50.
 
@@ -964,23 +920,20 @@ L3 programming layer <2026-01-19>
 
 LaTeX Warning: There were undefined references.
 
- )
-(\end occurred inside a group at level 3)
 
-### semi simple group (level 3) entered at line 27 (\begingroup)
+LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
-### semi simple group (level 2) entered at line 20 (\begingroup)
+
-### semi simple group (level 1) entered at line 6 (\begingroup)
+ ) 
-### bottom level 
 Here is how much of TeX's memory you used:
- 26181 strings out of 469514
+ 26246 strings out of 469514
- 551159 string characters out of 5469022
+ 552438 string characters out of 5469022
- 975555 words of memory out of 5000000
+ 984190 words of memory out of 5000000
- 54225 multiletter control sequences out of 15000+600000
+ 54290 multiletter control sequences out of 15000+600000
  683164 words of font info for 159 fonts, out of 8000000 for 9000
  14 hyphenation exceptions out of 8191
- 110i,9n,108p,1062b,1205s stack positions out of 10000i,1000n,20000p,200000b,200000s
+ 110i,9n,108p,1062b,960s stack positions out of 10000i,1000n,20000p,200000b,200000s
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-Output written on main.pdf (27 pages, 188487 bytes).
+Output written on main.pdf (27 pages, 190748 bytes).
 PDF statistics:
  180 PDF objects out of 1000 (max. 8388607)
  109 compressed objects within 2 object streams

main.tex

@@ -10,7 +10,7 @@
 % === SPLIT'S EDITING COMMENTS ===
 % Remove this block when done editing
 \usepackage[colorinlistoftodos,prependcaption,textsize=small]{todonotes}
-\newcommand{\split}[1]{\todo[color=green!40,author=Split]{#1}}
+\newcommand{\splitnote}[1]{\todo[color=green!40,author=Split]{#1}}
 \newcommand{\splitinline}[1]{\todo[inline,color=green!40,author=Split]{#1}}
 \setlength{\marginparwidth}{2.5cm}  % Make room for margin notes
 % ================================