A few fixes in manual

addresses #213

[makedoc]

CHANGES/v2.1.txt

@@ -30,7 +30,7 @@ character now has a special usage in component names.
   if these libraries are not installed.
 - New actions:
   - \ref SPRINT topological collective variables.
-  - \ref CH3SHIFTS collective variable.
+  - CH3SHIFTS collective variable.
   - \ref POSITION collective variable.
   - \ref FIT_TO_TEMPLATE.
   - \ref COMMITTOR analysis.

src/analysis/PCA.cpp

@@ -73,7 +73,7 @@ elements of the covariance matrix from the input vectors.  In this calculation t
 Trajectory frames will be collected every five steps and the PCA calculation is performed every 1000 steps.  Consequently, if you run a 2000 step simulation the 
 PCA analysis will be performed twice.  The REWEIGHT_BIAS keyword in this input tells PLUMED that rather that ascribing a weight of one to each of the frames
 when calculating averages and covariances a reweighting should be performed based and each frames' weight in these calculations should be determined based on 
-the current value of the instantaneous bias (see \ref reweighting).  
+the current value of the instantaneous bias (see \ref REWEIGHT_BIAS).  
 
 \verbatim
 d1: DISTANCE ATOMS=1,2

src/cltools/Driver.cpp

@@ -77,6 +77,8 @@ plumed driver-float --plumed plumed.dat --ixyz trajectory.xyz
 See also examples in \ref driver
 
 */
+//+ENDPLUMEDOC
+//
 
 
 //+PLUMEDOC TOOLS driver

src/multicolvar/FilterBetween.cpp

@@ -45,7 +45,7 @@ MEAN for \ref MFILTER_BETWEEN one is thus calculating:
 \mu = \frac{ \sum_i f_i s_i }{ \sum_i f_i}
 \f]
 
-In this action by contrast the colvar is being transformed by the \ref histogram bead.  If one thus calculates a MEAN for 
+In this action by contrast the colvar is being transformed by the \ref histogrambead.  If one thus calculates a MEAN for 
 thia action one computes:
 
 \f[

user-doc/Bias.txt

@@ -10,8 +10,5 @@ The list of enhanced sampling algorithms contained in PLUMED is as follows:
 Methods, such as \ref METAD or \ref PBMETAD, that work by introducing a history dependent bias can be restarted 
 using the \subpage RESTART keyword
 
-You can also use PLUMED in conjunction with VMD's interactive MD module by taking
-advantage of the \subpage IMD action.
-
 */