correct some more broken or outdated links

doc/src/Build_settings.txt

@@ -80,8 +80,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range
 Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
 communication can be costly).  A breakdown of these timings is printed
 to the screen at the end of a run using the "kspace_style
-pppm"_kspace_style.html command.  The "Run output"_doc page gives more
-details.
+pppm"_kspace_style.html command.  The "Run output"_Run_output.html
+doc page gives more details.
 
 FFTW is a fast, portable FFT library that should also work on any
 platform and can be faster than the KISS FFT library.  You can

doc/src/Packages_details.txt

@@ -1582,8 +1582,6 @@ molecular visualization and analysis program, to enable LAMMPS to dump
 snapshots in formats compatible with various molecular simulation
 tools.
 
-:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
-
 To use this package you must have the desired VMD plugins available on
 your system.
 
@@ -1635,6 +1633,7 @@ tools:
 "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
 
 :link(ovito,http://www.ovito.org)
+:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
 :link(atomeye,http://www.libatoms.org)
 
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).
@@ -1998,3 +1997,5 @@ src/USER-VTK: filenames -> commands
 src/USER-VTK/README
 lib/vtk/README
 "dump vtk"_dump_vtk.html :ul
+
+

doc/src/Packages_user.txt

@@ -58,7 +58,7 @@ Package, Description, Doc page, Example, Library
 "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
 "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
 "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
-"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
+"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
 "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
 "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no