docs: fix some broken links after update

docs/docs/user-guide/reading-files.md

@@ -2,7 +2,7 @@
 
 One of the main motivations behind ozzy is to be able to easily integrate different simulation file formats into the same plotting and analysis workflow (in this case with Python). In addition, we try to make it easy to add new backend instructions to ozzy to parse new file formats.
 
-Here is a list of simulation file formats that ozzy can read currently or which will be implemented soon (besides [ozzy's own format](../reference/backends/submodules/ozzy.md), of course):
+Here is a list of simulation file formats that ozzy can read currently or which will be implemented soon (besides [ozzy's own format](../reference/backends/ozzy.md), of course):
 
 <div class="annotate" markdown>
 
@@ -12,8 +12,8 @@ Here is a list of simulation file formats that ozzy can read currently or which
 
 </div>
 
-1.  Please see the reference page for the [OSIRIS backend submodule](../reference/backends/submodules/osiris.md) for more details. Not all types of simulation output may be available yet.
-2.  Please see the reference page for the [LCODE backend submodule](../reference/backends/submodules/lcode.md). Not all types of simulation output may be available yet.
+1.  Please see the reference page for the [OSIRIS backend submodule](../reference/backends/osiris.md) for more details. Not all types of simulation output may be available yet.
+2.  Please see the reference page for the [LCODE backend submodule](../reference/backends/lcode.md). Not all types of simulation output may be available yet.
 
 
 There are three main functions to open simulation files:

src/ozzy/part_mixin.py

@@ -621,10 +621,7 @@ def get_emittance(
         r"""Calculate normalized RMS beam emittance.
 
         Computes the normalized RMS emittance based on particle positions and momenta.
-        For axisymmetric beams, returns the Lapostolle[^1] emittance (see also Ref.[^2]).
-
-        [^1]: [J. D. Lawson, P. M. Lapostolle, and R. L. Gluckstern, Particle Accelerators **5**, 61–65 (1973)](https://inspirehep.net/literature/87013),
-        [^2]: [P. M. Lapostolle, IEEE Transactions on Nuclear Science **18**, 1101–1104 (1971)](https://ieeexplore-ieee-org.ezproxy.cern.ch/document/4326292)
+        For axisymmetric beams, returns the emittance (see _Notes_ below).
 
         Parameters
         ----------
@@ -652,11 +649,16 @@ def get_emittance(
 
         where $\gamma$ is the average Lorentz factor, $x_i$ is the particle position, and $x'_i \approx p_i / p_\parallel$ is the trace for relativistic particles with longitudinal momentum $p_\parallel$ and transverse momentum $p_i \ll p_\parallel$.
 
-        For a 2D cylindrical, axisymmetric geometry this function returns the Lapostolle emittance, i.e.:
+        For a 2D cylindrical, axisymmetric geometry this function returns the Lapostolle emittance[^1]<sup>,</sup>[^2], i.e.:
 
         $\varepsilon_N = 4 \ \varepsilon_{N,i}$
 
 
+        [^1]: [J. D. Lawson, P. M. Lapostolle, and R. L. Gluckstern, Particle Accelerators **5**, 61–65 (1973)](https://inspirehep.net/literature/87013),
+        [^2]: [P. M. Lapostolle, IEEE Transactions on Nuclear Science **18**, 1101–1104 (1971)](https://ieeexplore-ieee-org.ezproxy.cern.ch/document/4326292)
+
+
+
 
         Examples
         --------