Fix links in docs

Author: MalloryWittwer

docs/concepts/layers-and-stacks.md

@@ -2,7 +2,7 @@
 
 ## Data layers
 
-A **data layer** holds a single piece of data, such as an image, a segmentation mask, a set of points, or a numeric value, together with information about what that data means. All data layers derive from `sk.Layer`, and the available types are listed in [Data layers](../reference/layers.md).
+A **data layer** holds a single piece of data, such as an image, a segmentation mask, a set of points, or a numeric value, together with information about what that data means. All data layers derive from `sk.Layer`, and the available types are listed in [Data layers](../reference/api/layers.md).
 
 Data layers play two roles:
 

docs/how-to/live-updates.md

@@ -78,4 +78,4 @@ Here, the algorithm notifies the user that processing has started, then yields a
 - `sk.Notification` is used to show a message to the user. In Napari, it appears as a notification. You can set its level with `level="info"` (default), `"warning"`, or `"error"`.
 - `sk.Progress` updates a progress bar, up to `max_val`.
 
-See [Data layers](../reference/layers.md) for the other layer types.
+See [Data layers](../reference/api/layers.md) for the other layer types.

docs/how-to/tiling.md

@@ -80,4 +80,4 @@ def label_objects(image, threshold=128):
     return sk.Mask(labels, merger="instances")
 ```
 
-See [Tile merging](../concepts/coordinates.md#tile-merging) for how each layer type is assembled from tiles.
+See [Merging tiles](../concepts/coordinates.md#merging-tiles) for how each layer type is assembled from tiles.

docs/reference/api/layers.md

@@ -1,6 +1,6 @@
 # Data layers
 
-See [Data layers](../layers.md) for an overview of the available layers.
+See [Data layers](../../concepts/layers-and-stacks.md) for an introduction to data layers.
 
 ::: imaging_server_kit.Layer
     options:

docs/tutorial/create-algorithm.md

@@ -63,7 +63,7 @@ The algorithm works, but there is room for improvement. For example, nothing pre
 
 ## Annotating parameters
 
-Annotating parameters tells *Imaging Server Kit* how to interpret the function arguments. Each parameter is matched with a [data layer](../reference/layers.md), which is used to validate its value and to display it in user interfaces.
+Annotating parameters tells *Imaging Server Kit* how to interpret the function arguments. Each parameter is matched with a [data layer](../reference/api/layers.md), which is used to validate its value and to display it in user interfaces.
 
 Here is an improved version of the Gaussian filter, where `sigma` is annotated through `parameters={}` in the decorator, with a minimum and a default value:
 
@@ -85,7 +85,7 @@ In Napari, `sigma` can no longer be set to a negative value.
     - `step` (for UI sliders and spin boxes)
     - `name` (the label shown next to the parameter)
 
-    See [Data layers](../reference/layers.md) for the full list of layers.
+    See [Data layers](../reference/api/layers.md) for the full list of layers.
 
 `parameters={}` is the most explicit annotation method, but type hints, default values, and even variable names also work. All the following are valid:
 
@@ -106,7 +106,7 @@ def gaussian_algo(img: sk.Image, sigma: float):
     ...
 ```
 
-When several methods apply to the same parameter, explicit annotations take priority. See [Parameter resolution](../concepts/algorithms.md#parameter-resolution) for a full review of the rules.
+When several methods apply to the same parameter, explicit annotations take priority. See [Matching parameters with data layers](../concepts/algorithms.md#matching-parameters-with-data-layers) for a full review of the rules.
 
 ## Annotating return values
 

mkdocs.yml

@@ -140,7 +140,7 @@ extra:
     sections/06_tiled.html: how-to/tiling.md
     sections/07_server.html: tutorial/serve.md
     sections/08_python.html: tutorial/python.md
-    sections/09_layers.html: reference/layers.md
+    sections/09_layers.html: reference/api/layers.md
     sections/10_examples.html: examples.md
     sections/11_qupath.html: how-to/qupath.md
 

src/imaging_server_kit/merge/layer_merger.py

@@ -77,7 +77,7 @@ def merge_layers(layers: List[Layer]) -> Layer:
     """Merge a list of data layers of the same kind into a new layer.
 
     The layers are merged as successive tiles, following the merging strategy of the
-    layer type (see the "Tile merging" section of the documentation). The input layers
+    layer type (see the "Merging tiles" section of the documentation). The input layers
     are not modified.
 
     Parameters