diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html
index d62ccb2685..ff31520e64 100644
--- a/doc/Section_accelerate.html
+++ b/doc/Section_accelerate.html
@@ -513,10 +513,10 @@ that its sample projects can be compiled without problems.
 </P>
 <P>As with other packages that include a separately compiled library, you
 need to first build the USER-CUDA library, before building LAMMPS
-itself.  General instructions for doing this are in <A HREF = "doc/Section_start.html#start_3">this
-section</A> of the manual.  For this
-package, do the following, using settings in the lib/cuda Makefiles
-appropriate for your system:
+itself.  General instructions for doing this are in <A HREF = "Section_start.html#start_3">this
+section</A> of the manual.  For this package,
+do the following, using settings in the lib/cuda Makefiles appropriate
+for your system:
 </P>
 <UL><LI>Go to the lammps/lib/cuda directory 
 
diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt
index 240224cfb7..557ab159b3 100644
--- a/doc/Section_accelerate.txt
+++ b/doc/Section_accelerate.txt
@@ -514,9 +514,9 @@ that its sample projects can be compiled without problems.
 As with other packages that include a separately compiled library, you
 need to first build the USER-CUDA library, before building LAMMPS
 itself.  General instructions for doing this are in "this
-section"_doc/Section_start.html#start_3 of the manual.  For this
-package, do the following, using settings in the lib/cuda Makefiles
-appropriate for your system:
+section"_Section_start.html#start_3 of the manual.  For this package,
+do the following, using settings in the lib/cuda Makefiles appropriate
+for your system:
 
 Go to the lammps/lib/cuda directory :ulb,l
 
diff --git a/doc/compute_voronoi_atom.html b/doc/compute_voronoi_atom.html
index f6bad65549..ea31b5f279 100644
--- a/doc/compute_voronoi_atom.html
+++ b/doc/compute_voronoi_atom.html
@@ -59,7 +59,7 @@ This should still work for a 2d LAMMPS simulation, to effectively
 compute Vornoi "areas", so long as the z-dimension of the box is
 roughly the same (or smaller) compared to the separation of the atoms.
 Typical values for the z box dimensions in a 2d LAMMPS model are -0.5
-to 0.5, which satisfies the criterion for most <A HREF = "doc/units.html">units</A>
+to 0.5, which satisfies the criterion for most <A HREF = "units.html">units</A>
 systems.  Note that you define the z extent of the simulation box for
 2d simulations when using the <A HREF = "create_box.html">create_box</A> or
 <A HREF = "read_data.html">read_data</A> commands.
diff --git a/doc/compute_voronoi_atom.txt b/doc/compute_voronoi_atom.txt
index dac1d2e726..cfa1258fa0 100644
--- a/doc/compute_voronoi_atom.txt
+++ b/doc/compute_voronoi_atom.txt
@@ -56,7 +56,7 @@ This should still work for a 2d LAMMPS simulation, to effectively
 compute Vornoi "areas", so long as the z-dimension of the box is
 roughly the same (or smaller) compared to the separation of the atoms.
 Typical values for the z box dimensions in a 2d LAMMPS model are -0.5
-to 0.5, which satisfies the criterion for most "units"_doc/units.html
+to 0.5, which satisfies the criterion for most "units"_units.html
 systems.  Note that you define the z extent of the simulation box for
 2d simulations when using the "create_box"_create_box.html or
 "read_data"_read_data.html commands.
diff --git a/doc/dump.html b/doc/dump.html
index 6a70fa0476..1d802308b9 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -171,7 +171,7 @@ characters that encode the style of boundary for each of the 6
 simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi).  Each of
 the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
 or m = shrink wrapped with a minimum value.  See the
-<A HREF = "doc/boundary.html">boundary</A> command for details.
+<A HREF = "boundary.html">boundary</A> command for details.
 </P>
 <P>For triclinic simulation boxes (non-orthogonal), an orthogonal
 bounding box which encloses the triclinic simulation box is output,
diff --git a/doc/dump.txt b/doc/dump.txt
index 9d3538c275..42d1f35cd8 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -159,7 +159,7 @@ characters that encode the style of boundary for each of the 6
 simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi).  Each of
 the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
 or m = shrink wrapped with a minimum value.  See the
-"boundary"_doc/boundary.html command for details.
+"boundary"_boundary.html command for details.
 
 For triclinic simulation boxes (non-orthogonal), an orthogonal
 bounding box which encloses the triclinic simulation box is output,
diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html
index 28b0d9cb40..432851d4d7 100644
--- a/doc/fix_adapt.html
+++ b/doc/fix_adapt.html
@@ -165,7 +165,7 @@ asterisks imply type pairs where J < I, they are ignored.
 <P>IMPROTANT NOTE: If <A HREF = "pair_hybrid.html">pair_style hybrid or
 hybrid/overlay</A> is being used, then the <I>pstyle</I> will
 be a sub-style name.  You must specify I,J arguments that correspond
-to type pair values defined (via the <A HREF = "doc/pair_coeff.html">pair_coeff</A>
+to type pair values defined (via the <A HREF = "pair_coeff.html">pair_coeff</A>
 command) for that sub-style.
 </P>
 <P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
diff --git a/doc/fix_adapt.txt b/doc/fix_adapt.txt
index bd9bc5a9a7..959aaeb5d6 100644
--- a/doc/fix_adapt.txt
+++ b/doc/fix_adapt.txt
@@ -151,7 +151,7 @@ asterisks imply type pairs where J < I, they are ignored.
 IMPROTANT NOTE: If "pair_style hybrid or
 hybrid/overlay"_pair_hybrid.html is being used, then the {pstyle} will
 be a sub-style name.  You must specify I,J arguments that correspond
-to type pair values defined (via the "pair_coeff"_doc/pair_coeff.html
+to type pair values defined (via the "pair_coeff"_pair_coeff.html
 command) for that sub-style.
 
 The {v_name} argument for keyword {pair} is the name of an