Fix unlinked module names in Doxygen file list descriptions

Use explicit @ref for mixed-case Fortran modules (m_bubbles_EE/EL/
EL_kernels) so Doxygen resolves the lowercase namespace. Correct
wrong module names in @file briefs: m_boundary_conditions_common ->
m_boundary_common, m_patches -> m_ib_patches / m_icpp_patches.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

src/common/m_boundary_common.fpp

@@ -1,6 +1,6 @@
 !>
 !! @file
-!! @brief Contains module m_boundary_conditions_common
+!! @brief Contains module m_boundary_common
 
 !> @brief The purpose of the module is to apply noncharacteristic and processor
 !! boundary conditions

src/pre_process/m_icpp_patches.fpp

@@ -1,6 +1,6 @@
 !>
 !! @file
-!! @brief Contains module m_patches
+!! @brief Contains module m_icpp_patches
 
 #:include 'case.fpp'
 #:include 'ExtrusionHardcodedIC.fpp'

src/simulation/m_bubbles_EE.fpp

@@ -1,6 +1,6 @@
 !>
 !! @file
-!! @brief Contains module m_bubbles_EE
+!! @brief Contains module @ref m_bubbles_ee "m_bubbles_EE"
 
 #:include 'macros.fpp'
 

src/simulation/m_bubbles_EL.fpp

@@ -1,6 +1,6 @@
 !>
 !! @file
-!! @brief Contains module m_bubbles_EL
+!! @brief Contains module @ref m_bubbles_el "m_bubbles_EL"
 
 #:include 'macros.fpp'
 

src/simulation/m_bubbles_EL_kernels.fpp

@@ -1,6 +1,6 @@
 !>
 !! @file
-!! @brief Contains module m_bubbles_EL_kernels
+!! @brief Contains module @ref m_bubbles_el_kernels "m_bubbles_EL_kernels"
 
 #:include 'macros.fpp'
 

src/simulation/m_ib_patches.fpp

@@ -1,6 +1,6 @@
 !>
 !! @file
-!! @brief Contains module m_patches
+!! @brief Contains module m_ib_patches
 
 #:include 'case.fpp'
 #:include 'ExtrusionHardcodedIC.fpp'