awk only solution (tested with gawk):

$ awk ' BEGIN { footer = ""; } END { while(( getline line < "sol.txt") > 0 ) { print(line) } print substr(footer, 0, length(footer)-1); } # Blank line or comment-only (/^[[:blank:]]*#/ || /^[[:blank:]]*$/) { footer = footer $0 "\n"; } # Configuration line /^[[:blank:]]*[^[:space:]#]/ { print(footer $0); footer = ""; } ' < universe.txt > universe2.txt 

Producing:

# Universe configuration # pi = 3 # A good # e = mc**2 # To within a hair [cut 200 trillion lines] sol { mass = 42, start = 9.2 } # # END # 

With one line diff:

sh$ diff universe*.txt 8d7 < sol { mass = 42, start = 9.2 } 

awk only solution (tested with gawk):

$ awk ' BEGIN { footer = ""; wl = ""; } END { while(( getline line < "sol.txt") > 0 ) { print(line) } footer = wl footer print substr(footer, 0, length(footer)-1); } # Blank line /^[[:blank:]]*$/ { if (footer) { footer = wl footer print substr(footer, 0, length(footer)-1); footer = "" } wl = $0 "\n" } # Comment only /^[[:blank:]]*#/ { footer = footer $0 "\n"; } # Configuration line /^[[:blank:]]*[^[:space:]#]/ { print(wl footer $0); wl = ""; footer = ""; } ' < universe.txt > universe2.txt 

Producing:

# Universe configuration # pi = 3 # A good # e = mc**2 # To within a hair [cut 200 trillion lines] sol { mass = 42, start = 9.2 } # # END # 

With one line diff:

sh$ diff universe*.txt 8d7 < sol { mass = 42, start = 9.2 } 

awk only solution (tested with gawk):

$ awk ' BEGIN { comment = ""; }  /^#/ { comment = comment $0 "\n"; } END { while(( getline line < "sol.txt") > 0 ) { print(line) } print substr(comment, 0, length(comment)-1); } /^[^#]/ || /^$/ { print(comment $0); comment = ""; } ' < universe.txt 

Producing:

# Universe configuration # pi = 3 # A good # e = mc**2 # To within a hair [cut 200 trillion lines]   sol { mass = 42, start = 9.2 } # # END # 

awk only solution (tested with gawk):

$ awk ' BEGIN { footer = ""; } END { while(( getline line < "sol.txt") > 0 ) { print(line) } print substr(footer, 0, length(footer)-1);  }     # Blank line or comment-only (/^[[:blank:]]*#/ || /^[[:blank:]]*$/) { footer = footer $0 "\n"; }  # Configuration line /^[[:blank:]]*[^[:space:]#]/ { print(footer $0); footer = "";  } ' < universe.txt > universe2.txt 

Producing:

# Universe configuration # pi = 3 # A good # e = mc**2 # To within a hair [cut 200 trillion lines] sol { mass = 42, start = 9.2 }   # # END # 

With one line diff:

sh$ diff universe*.txt 8d7 < sol { mass = 42, start = 9.2 }