diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html
index 38a2120019..d62ccb2685 100644
--- a/doc/Section_accelerate.html
+++ b/doc/Section_accelerate.html
@@ -370,10 +370,10 @@ hardware and install specific NVIDIA CUDA software on your system:
 </P>
 <P>As with other packages that include a separately compiled library, you
 need to first build the GPU 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 a Makefile in lib/gpu appropriate for
-your system:
+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 a Makefile in lib/gpu appropriate for your
+system:
 </P>
 <PRE>cd lammps/lib/gpu
 make -f Makefile.linux
diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt
index bc8cc0e4bf..240224cfb7 100644
--- a/doc/Section_accelerate.txt
+++ b/doc/Section_accelerate.txt
@@ -371,9 +371,9 @@ Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties :ul
 As with other packages that include a separately compiled library, you
 need to first build the GPU 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 a Makefile in lib/gpu appropriate for
-your system:
+section"_Section_start.html#start_3 of the manual.  For this package,
+do the following, using a Makefile in lib/gpu appropriate for your
+system:
 
 cd lammps/lib/gpu
 make -f Makefile.linux
diff --git a/doc/Section_example.html b/doc/Section_example.html
index 6881f186d0..9bc646d0bc 100644
--- a/doc/Section_example.html
+++ b/doc/Section_example.html
@@ -113,7 +113,8 @@ the in.elastic file for more info.
 </P>
 <P>There is also a USER directory which contains subdirectories of
 user-provided examples for user packages.  See the README files in
-those directories for more info.  See the doc/Section_start.html file
-for more info about user packages.
+those directories for more info.  See the
+<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
+packages.
 </P>
 </HTML>
diff --git a/doc/Section_example.txt b/doc/Section_example.txt
index 6de3268e40..ac2cc47b72 100644
--- a/doc/Section_example.txt
+++ b/doc/Section_example.txt
@@ -108,5 +108,6 @@ the in.elastic file for more info.
 
 There is also a USER directory which contains subdirectories of
 user-provided examples for user packages.  See the README files in
-those directories for more info.  See the doc/Section_start.html file
-for more info about user packages.
+those directories for more info.  See the
+"Section_start.html"_Section_start.html file for more info about user
+packages.
diff --git a/doc/Section_intro.html b/doc/Section_intro.html
index 3e7cbe07bd..ec7d4996a9 100644
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@@ -253,7 +253,7 @@ molecular dynamics options:
 <LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
 <LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
 <LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
-<LI><A HREF = "doc/fix_gcmc.html">grand canonical Monte Carlo</A> insertions/deletions
+<LI><A HREF = "fix_gcmc.html">grand canonical Monte Carlo</A> insertions/deletions
 <LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
 <LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
 <LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index 4d415ac98f..fd2f491065 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -249,7 +249,7 @@ molecular dynamics options:
 "real-time visualization and interactive MD"_fix_imd.html
 "atom-to-continuum coupling"_fix_atc.html with finite elements
 coupled rigid body integration via the "POEMS"_fix_poems.html library
-"grand canonical Monte Carlo"_doc/fix_gcmc.html insertions/deletions
+"grand canonical Monte Carlo"_fix_gcmc.html insertions/deletions
 "Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
 "Peridynamics mesoscale modeling"_pair_peri.html
 "targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
diff --git a/doc/fix_spring.html b/doc/fix_spring.html
index 8830056177..80d6d695df 100644
--- a/doc/fix_spring.html
+++ b/doc/fix_spring.html
@@ -100,7 +100,7 @@ can cross a periodic boundary and its length be calculated correctly.
 One exception is for rigid bodies, which should not be used with the
 fix spring command, if the rigid body will cross a periodic boundary.
 This is because image flags for rigid bodies are used in a different
-way, as explained on the <A HREF = "doc/fix_rigid.html">fix rigid</A> doc page.
+way, as explained on the <A HREF = "fix_rigid.html">fix rigid</A> doc page.
 </P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
diff --git a/doc/fix_spring.txt b/doc/fix_spring.txt
index 9b65065714..49e0818806 100644
--- a/doc/fix_spring.txt
+++ b/doc/fix_spring.txt
@@ -93,7 +93,7 @@ can cross a periodic boundary and its length be calculated correctly.
 One exception is for rigid bodies, which should not be used with the
 fix spring command, if the rigid body will cross a periodic boundary.
 This is because image flags for rigid bodies are used in a different
-way, as explained on the "fix rigid"_doc/fix_rigid.html doc page.
+way, as explained on the "fix rigid"_fix_rigid.html doc page.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
diff --git a/doc/read_restart.html b/doc/read_restart.html
index 0b012647c0..2c76ce6bf9 100644
--- a/doc/read_restart.html
+++ b/doc/read_restart.html
@@ -109,7 +109,7 @@ restart files.  The doc pages for individual pair styles note if this
 is the case.  This is also true of bond_style hybrid (and angle_style,
 dihedral_style, improper_style hybrid).
 </P>
-<P>All settings made by the <A HREF = "doc/pair_modify.html">pair_modify</A> command,
+<P>All settings made by the <A HREF = "pair_modify.html">pair_modify</A> command,
 such as the shift and tail settings, are stored in the restart file
 with the pair style.  The one exception is the <A HREF = "pair_modify.html">pair_modify
 compute</A> setting is not stored.
@@ -146,9 +146,9 @@ bonds will still be broken when the restart file is read.
 <P>IMPORTANT NOTE: No other information is stored in the restart file.
 This means that an input script that reads a restart file should
 specify settings for quantities like <A HREF = "timestep.html">timestep size</A>,
-<A HREF = "thermo_style.html">thermodynamic</A>, <A HREF = "doc/neighbor.html">neighbor list</A>
+<A HREF = "thermo_style.html">thermodynamic</A>, <A HREF = "neighbor.html">neighbor list</A>
 criteria including settings made via the
-<A HREF = "doc/neigh_modify.html">neigh_modify</A> comand, <A HREF = "dump.html">dump</A> file
+<A HREF = "neigh_modify.html">neigh_modify</A> comand, <A HREF = "dump.html">dump</A> file
 output, <A HREF = "region.html">geometric regions</A>, etc.
 </P>
 <HR>
diff --git a/doc/read_restart.txt b/doc/read_restart.txt
index 5431855eb4..cc7a95d656 100644
--- a/doc/read_restart.txt
+++ b/doc/read_restart.txt
@@ -106,7 +106,7 @@ restart files.  The doc pages for individual pair styles note if this
 is the case.  This is also true of bond_style hybrid (and angle_style,
 dihedral_style, improper_style hybrid).
 
-All settings made by the "pair_modify"_doc/pair_modify.html command,
+All settings made by the "pair_modify"_pair_modify.html command,
 such as the shift and tail settings, are stored in the restart file
 with the pair style.  The one exception is the "pair_modify
 compute"_pair_modify.html setting is not stored.
@@ -143,9 +143,9 @@ bonds will still be broken when the restart file is read.
 IMPORTANT NOTE: No other information is stored in the restart file.
 This means that an input script that reads a restart file should
 specify settings for quantities like "timestep size"_timestep.html,
-"thermodynamic"_thermo_style.html, "neighbor list"_doc/neighbor.html
+"thermodynamic"_thermo_style.html, "neighbor list"_neighbor.html
 criteria including settings made via the
-"neigh_modify"_doc/neigh_modify.html comand, "dump"_dump.html file
+"neigh_modify"_neigh_modify.html comand, "dump"_dump.html file
 output, "geometric regions"_region.html, etc.
 
 :line