Refactor documentation structure by removing redundant summary and ad…

…ding section dividers for improved readability

docs/source/output.md

@@ -118,5 +118,3 @@ MTase-linker uses external tools for gene prediction and annotation:
 - **All predicted protein sequences:** `.../prodigal/{assembly_name}_processed.faa` contains amino acid sequences for all predicted proteins, including MTases.
 
 ---
-
-**In summary**, these outputs provide a comprehensive overview of methylation motifs, bin quality, contamination checks, and the linkage between motifs and MTase genes. By reviewing the columns and their meanings, you can more easily interpret these results in the context of your analyses.

docs/source/usage.md

@@ -1,5 +1,7 @@
 # Usage
 
+---
+
 ## Motif discovery
 
 Motif discovery is meant for identifying motif at contig and bin level. It consist of three commands `find_motifs`, `score_motifs` & `bin_consensus`. We provide a wrapper command that executes these three commands togehter; `motif_discovery`.
@@ -49,6 +51,8 @@ optional arguments:
 ```
 
 
+---
+
 ## Bin improvement
 
 ### Bin contamination
@@ -109,6 +113,7 @@ Mandatory Arguments:
   --contig_bins CONTIG_BINS
                         Path to bins.tsv file for contig bins
   --out OUT             Path to output directory```
+```
 
 The output is a `bin_contamination.tsv` file. The each contaminant will have 4 rows, one for each clustering algorithm, along with the cluster stats.
 
@@ -185,6 +190,9 @@ Mandatory Arguments:
   --contig_bins CONTIG_BINS
                         Path to bins.tsv file for contig bins
   --out OUT             Path to output directory```
+```
+
+---
 
 ## MTase-linker