diff --git a/CLAUDE.md b/CLAUDE.md
index 46e62f08..514b552f 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -56,12 +56,13 @@ uv run jabs-cli --help                     # Unified CLI utilities
 
 # Standalone CLI scripts
 uv run jabs-init /path/to/project          # Initialize a JABS project
-uv run jabs-features /path/to/project      # Generate features (batch, no GUI)
 uv run jabs-classify --classifier model.pkl /path/to/pose.h5  # Batch classification
 uv run jabs-stats /path/to/project         # View project statistics
 
 # jabs-cli subcommands (preferred for new utilities)
+uv run jabs-cli compute-features           # Generate features for a pose file (batch, no GUI)
 uv run jabs-cli export-training            # Export training data from a project
+uv run jabs-cli merge                      # Merge one JABS project into another
 uv run jabs-cli rename-behavior            # Rename a behavior across a project
 uv run jabs-cli prune                      # Remove videos from a project
 ```
diff --git a/docs/development/development.md b/docs/development/development.md
index 8984a782..3dea9673 100644
--- a/docs/development/development.md
+++ b/docs/development/development.md
@@ -938,8 +938,8 @@ jabs
 # Initialize a JABS project
 jabs-init /path/to/project
 
-# Generate features for an HDF5 file without requring a JABS project (for batch processing)
-jabs-features /path/to/project
+# Generate features for a pose file without requiring a JABS project (for batch processing)
+jabs-cli compute-features --pose-file /path/to/pose_file.h5 --feature-dir /path/to/features
 
 # Run batch classification
 jabs-classify --classifier my_classifier.pkl /path/to/pose_file.h5
@@ -958,8 +958,10 @@ jabs-cli --help
 `jabs-cli` is a unified command-line interface that consolidates smaller JABS utilities under a single entry point. Instead of having many separate standalone scripts, `jabs-cli` uses Click's group/command pattern to organize related functionality.
 
 **Current commands:**
+- `jabs-cli compute-features` - Compute and cache features for a single pose file
 - `jabs-cli convert-parquet` - Convert a parquet pose file to JABS HDF5 pose format
 - `jabs-cli export-training` - Export training data from a project
+- `jabs-cli merge` - Merge one JABS project into another
 - `jabs-cli rename-behavior` - Rename a behavior across a project
 - `jabs-cli prune` - Remove videos from a project based on criteria
 
@@ -1001,9 +1003,10 @@ See existing commands in `cli.py` for complete examples.
 
 Some standalone scripts may be deprecated in favor of expanding `jabs-cli`. Candidates (non-exhaustive) for consolidation include:
 - `jabs-init` → `jabs-cli init-project`
-- `jabs-project-merge` → `jabs-cli merge`
 
-This consolidation would provide a more cohesive user experience and easier maintenance. However, backward compatibility will be maintained during any transition period.
+The former `jabs-project-merge` script has already been consolidated as `jabs-cli merge`; the standalone entry point was removed.
+
+This consolidation would provide a more cohesive user experience and easier maintenance.
 
 **When to create a standalone script:**
 
diff --git a/docs/user-guide/cli-tools.md b/docs/user-guide/cli-tools.md
index 6957a640..b0b84e2b 100644
--- a/docs/user-guide/cli-tools.md
+++ b/docs/user-guide/cli-tools.md
@@ -80,32 +80,19 @@ optionally override the classifier specified in the training file:
 
 ## jabs-features
 
-JABS includes a script called `jabs-features`, which can be used to generate a feature file for a single video from the command line.
+**Deprecated.** `jabs-features` has been replaced by [`jabs-cli compute-features`](#jabs-cli-compute-features). The command still works, but it prints a deprecation warning, translates its arguments, and runs `jabs-cli compute-features` for you. Update existing pipelines to call the new command directly.
 
-```text
-usage: jabs-features [-h] --pose-file POSE_FILE --pose-version POSE_VERSION
-                            --feature-dir FEATURE_DIR [--use-cm-distances]
-                            [--window-size WINDOW_SIZE] [--fps FPS]
-                            [--use-pose-hash]
-
-options:
-  -h, --help            show this help message and exit
-  --pose-file POSE_FILE
-                        pose file to compute features for
-  --pose-version POSE_VERSION
-                        pose version to calculate features
-  --feature-dir FEATURE_DIR
-                        directory to write output features
-  --use-cm-distances    use cm distance units instead of pixel
-  --window-size WINDOW_SIZE
-                        window size for features (default none)
-  --fps FPS             frames per second to use for feature calculation
-  --use-pose-hash       Include the pose file hash as a subdirectory level in the feature cache
-                        path (e.g. <feature-dir>/<video>/<pose-hash>/<identity>). Prevents
-                        collisions when a shared cache directory is used across multiple pipelines.
-```
+The legacy options map onto the new command as follows:
 
-Features are always written in Parquet format. Use `--use-pose-hash` when building a shared feature cache for multiple pipelines where video filenames may collide.
+| `jabs-features` | `jabs-cli compute-features` |
+| --- | --- |
+| `--pose-file` | `--pose-file` (unchanged) |
+| `--pose-version` | Ignored. The pose version is inferred from the pose filename (e.g. `*_pose_est_v6.h5`). |
+| `--feature-dir` | `--feature-dir` (unchanged) |
+| `--use-cm-distances` | Not needed. Distances default to cm when the pose file provides a pixel-to-cm scale. Omitting `--use-cm-distances` maps to `--use-pixel-distances`, preserving the legacy pixel default. |
+| `--window-size N` | `-w N` (repeatable for multiple window sizes) |
+| `--fps` | `--fps` (unchanged) |
+| `--use-pose-hash` | `--use-pose-hash` (unchanged) |
 
 ## jabs-cli
 
@@ -125,11 +112,13 @@ Options:
   --help     Show this message and exit.
 
 Commands:
+  compute-features      Compute and cache JABS features for a pose file.
   convert-parquet       Convert a parquet pose file to JABS HDF5 pose format.
   postprocess           Apply a postprocessing pipeline to a JABS prediction HDF5 file.
   convert-to-nwb        Convert a JABS pose HDF5 file to NWB format.
   cross-validation      Run leave-one-group-out cross-validation for a JABS project.
   export-training       Export training data for a specified behavior and JABS project directory.
+  merge                 Merge one JABS project into another.
   prune                 Prune unused videos from a JABS project directory.
   rename-behavior       Rename a behavior in a JABS project.
   sample-frames         Sample PNG frames from a JABS project filtered by a behavior label.
@@ -181,6 +170,42 @@ jabs-init /path/to/project --cache-format parquet --force
 
 See the [Project Setup Guide](project-setup.md#initialization--jabs-init) for a brief overview and [Feature Cache Format](project-setup.md#feature-cache-format) for migration guidance.
 
+## jabs-cli compute-features
+
+The `jabs-cli compute-features` command computes and caches JABS features for a single pose file, without requiring a JABS project. This is intended for batch and HPC pipelines that process pose files individually. It replaces the deprecated [`jabs-features`](#jabs-features) script.
+
+**Usage:**
+
+```bash
+jabs-cli compute-features --pose-file <POSE_FILE> --feature-dir <FEATURE_DIR> [--use-pixel-distances]
+                          [-w WINDOW_SIZE] [--fps FPS] [--use-pose-hash]
+                          [--cache-format {hdf5,parquet}] [--force]
+```
+
+- `--pose-file <POSE_FILE>`: Pose file to compute features for. The pose version is inferred from the filename (e.g. `*_pose_est_v6.h5`).
+- `--feature-dir <FEATURE_DIR>`: Directory to write output features.
+- `--use-pixel-distances`: Force pixel distance units. By default, cm units are used when the pose file provides a pixel-to-cm scale, and pixel units otherwise.
+- `-w`, `--window-size <N>`: Window size for window features. Repeat to compute multiple window sizes (e.g. `-w 5 -w 10`). Omit to compute per-frame features only.
+- `--fps <FPS>`: Frames per second used to scale time-based features from "per frame" to "per second". Default: `30`.
+- `--use-pose-hash`: Include the pose file hash as a subdirectory level in the feature cache path (e.g. `<feature-dir>/<video>/<pose-hash>/<identity>`). Use this when building a shared feature cache for multiple pipelines where video filenames may collide.
+- `--cache-format {hdf5,parquet}`: Storage format for the feature cache. Default: `parquet`.
+- `--force`: Recompute features and overwrite the cache even when a valid cache exists.
+
+**Examples:**
+
+```bash
+# Per-frame features only
+jabs-cli compute-features --pose-file session_pose_est_v6.h5 --feature-dir /path/to/features
+
+# Per-frame plus two window sizes, at 60 fps
+jabs-cli compute-features --pose-file session_pose_est_v6.h5 --feature-dir /path/to/features \
+    -w 5 -w 10 --fps 60
+
+# Shared cache across pipelines, forcing recomputation
+jabs-cli compute-features --pose-file session_pose_est_v6.h5 --feature-dir /shared/features \
+    --use-pose-hash --force
+```
+
 ## jabs-cli update-pose
 
 The `jabs-cli update-pose` command updates an existing JABS project to use updated pose files for the same videos while remapping existing labels onto the updated poses. This is intended for keeping labels when pose files have been regenerated or otherwise updated.
@@ -250,6 +275,35 @@ jabs-cli update-labels /path/to/target_project /path/to/source_project --min-iou
 
 If instead you want to replace the target's pose while keeping its labels, see [`jabs-cli update-pose`](#jabs-cli-update-pose).
 
+## jabs-cli merge
+
+The `jabs-cli merge` command merges a source JABS project into a destination JABS project. Videos, pose files, behaviors, and labels from the source project are imported into the destination project, which is modified in place. The source project is left unchanged.
+
+Note: this command was previously the standalone `jabs-project-merge` script, which has been removed.
+
+**Usage:**
+
+```bash
+jabs-cli merge <destination_project> <source_project> --merge-strategy <STRATEGY>
+```
+
+- `<destination_project>`: Path to the destination JABS project. This project is modified by importing videos and labels from the source project.
+- `<source_project>`: Path to the source JABS project. Not modified.
+- `--merge-strategy <STRATEGY>`: Required. How to resolve conflicting labels, i.e. frames labeled differently in both projects for the same video, identity, and behavior:
+    - `behavior-wins`: Keep the label with the behavior annotation.
+    - `not-behavior-wins`: Keep the label without the behavior annotation.
+    - `destination-wins`: Keep the label from the destination project.
+
+Videos present only in the source project are copied into the destination project along with their pose files, and behaviors defined only in the source project are added to the destination project's `project.json`. Labels for videos already in the destination project are merged annotation by annotation using the selected strategy.
+
+Both paths must already be valid JABS project directories, and they must be different directories.
+
+**Example:**
+
+```bash
+jabs-cli merge /path/to/destination_project /path/to/source_project --merge-strategy destination-wins
+```
+
 ## jabs-cli sample-frames
 
 The `jabs-cli sample-frames` command extracts individual video frames as PNG images
diff --git a/pyproject.toml b/pyproject.toml
index b6fe3f00..f3da20e2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,6 @@ dependencies = [
   "xgboost>=2.0.0,<3.0.0",
   "pyarrow>=23.0.1,<24.0.0",
   "rich>=14.0.0,<15.0.0",
-  "rich-argparse>=1.7.1,<2.0.0",
   "intervaltree>=3.1.0,<4.0.0",
   "qt-material-icons>=0.2.0,<0.3.0",
   "jsonschema>=4.25.1,<5.0.0",
@@ -87,7 +86,6 @@ jabs = "jabs.scripts.gui_entrypoint:main"
 "jabs-classify" = "jabs.scripts.classify:main"
 "jabs-init" = "jabs.scripts.initialize_project:main"
 "jabs-features" = "jabs.scripts.generate_features:main"
-"jabs-project-merge" = "jabs.scripts.merge_projects:main"
 "jabs-cli" = "jabs.scripts.cli:main"
 
 [tool.uv.workspace]
diff --git a/ruff.toml b/ruff.toml
index b468269d..de38bc81 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -46,3 +46,7 @@ convention = "google"
 "src/jabs/scripts/cli/sample_frames.py" = [
     "D301",  # Click uses \b in docstrings to control help formatting
 ]
+"src/jabs/scripts/cli/merge_projects.py" = [
+    "D301",  # Click uses \b in docstrings to control help formatting
+    "D412",  # Click Examples sections look better with a blank line before \b blocks
+]
diff --git a/src/jabs/resources/docs/user_guide/cli-tools.md b/src/jabs/resources/docs/user_guide/cli-tools.md
index 6957a640..b0b84e2b 100644
--- a/src/jabs/resources/docs/user_guide/cli-tools.md
+++ b/src/jabs/resources/docs/user_guide/cli-tools.md
@@ -80,32 +80,19 @@ optionally override the classifier specified in the training file:
 
 ## jabs-features
 
-JABS includes a script called `jabs-features`, which can be used to generate a feature file for a single video from the command line.
+**Deprecated.** `jabs-features` has been replaced by [`jabs-cli compute-features`](#jabs-cli-compute-features). The command still works, but it prints a deprecation warning, translates its arguments, and runs `jabs-cli compute-features` for you. Update existing pipelines to call the new command directly.
 
-```text
-usage: jabs-features [-h] --pose-file POSE_FILE --pose-version POSE_VERSION
-                            --feature-dir FEATURE_DIR [--use-cm-distances]
-                            [--window-size WINDOW_SIZE] [--fps FPS]
-                            [--use-pose-hash]
-
-options:
-  -h, --help            show this help message and exit
-  --pose-file POSE_FILE
-                        pose file to compute features for
-  --pose-version POSE_VERSION
-                        pose version to calculate features
-  --feature-dir FEATURE_DIR
-                        directory to write output features
-  --use-cm-distances    use cm distance units instead of pixel
-  --window-size WINDOW_SIZE
-                        window size for features (default none)
-  --fps FPS             frames per second to use for feature calculation
-  --use-pose-hash       Include the pose file hash as a subdirectory level in the feature cache
-                        path (e.g. <feature-dir>/<video>/<pose-hash>/<identity>). Prevents
-                        collisions when a shared cache directory is used across multiple pipelines.
-```
+The legacy options map onto the new command as follows:
 
-Features are always written in Parquet format. Use `--use-pose-hash` when building a shared feature cache for multiple pipelines where video filenames may collide.
+| `jabs-features` | `jabs-cli compute-features` |
+| --- | --- |
+| `--pose-file` | `--pose-file` (unchanged) |
+| `--pose-version` | Ignored. The pose version is inferred from the pose filename (e.g. `*_pose_est_v6.h5`). |
+| `--feature-dir` | `--feature-dir` (unchanged) |
+| `--use-cm-distances` | Not needed. Distances default to cm when the pose file provides a pixel-to-cm scale. Omitting `--use-cm-distances` maps to `--use-pixel-distances`, preserving the legacy pixel default. |
+| `--window-size N` | `-w N` (repeatable for multiple window sizes) |
+| `--fps` | `--fps` (unchanged) |
+| `--use-pose-hash` | `--use-pose-hash` (unchanged) |
 
 ## jabs-cli
 
@@ -125,11 +112,13 @@ Options:
   --help     Show this message and exit.
 
 Commands:
+  compute-features      Compute and cache JABS features for a pose file.
   convert-parquet       Convert a parquet pose file to JABS HDF5 pose format.
   postprocess           Apply a postprocessing pipeline to a JABS prediction HDF5 file.
   convert-to-nwb        Convert a JABS pose HDF5 file to NWB format.
   cross-validation      Run leave-one-group-out cross-validation for a JABS project.
   export-training       Export training data for a specified behavior and JABS project directory.
+  merge                 Merge one JABS project into another.
   prune                 Prune unused videos from a JABS project directory.
   rename-behavior       Rename a behavior in a JABS project.
   sample-frames         Sample PNG frames from a JABS project filtered by a behavior label.
@@ -181,6 +170,42 @@ jabs-init /path/to/project --cache-format parquet --force
 
 See the [Project Setup Guide](project-setup.md#initialization--jabs-init) for a brief overview and [Feature Cache Format](project-setup.md#feature-cache-format) for migration guidance.
 
+## jabs-cli compute-features
+
+The `jabs-cli compute-features` command computes and caches JABS features for a single pose file, without requiring a JABS project. This is intended for batch and HPC pipelines that process pose files individually. It replaces the deprecated [`jabs-features`](#jabs-features) script.
+
+**Usage:**
+
+```bash
+jabs-cli compute-features --pose-file <POSE_FILE> --feature-dir <FEATURE_DIR> [--use-pixel-distances]
+                          [-w WINDOW_SIZE] [--fps FPS] [--use-pose-hash]
+                          [--cache-format {hdf5,parquet}] [--force]
+```
+
+- `--pose-file <POSE_FILE>`: Pose file to compute features for. The pose version is inferred from the filename (e.g. `*_pose_est_v6.h5`).
+- `--feature-dir <FEATURE_DIR>`: Directory to write output features.
+- `--use-pixel-distances`: Force pixel distance units. By default, cm units are used when the pose file provides a pixel-to-cm scale, and pixel units otherwise.
+- `-w`, `--window-size <N>`: Window size for window features. Repeat to compute multiple window sizes (e.g. `-w 5 -w 10`). Omit to compute per-frame features only.
+- `--fps <FPS>`: Frames per second used to scale time-based features from "per frame" to "per second". Default: `30`.
+- `--use-pose-hash`: Include the pose file hash as a subdirectory level in the feature cache path (e.g. `<feature-dir>/<video>/<pose-hash>/<identity>`). Use this when building a shared feature cache for multiple pipelines where video filenames may collide.
+- `--cache-format {hdf5,parquet}`: Storage format for the feature cache. Default: `parquet`.
+- `--force`: Recompute features and overwrite the cache even when a valid cache exists.
+
+**Examples:**
+
+```bash
+# Per-frame features only
+jabs-cli compute-features --pose-file session_pose_est_v6.h5 --feature-dir /path/to/features
+
+# Per-frame plus two window sizes, at 60 fps
+jabs-cli compute-features --pose-file session_pose_est_v6.h5 --feature-dir /path/to/features \
+    -w 5 -w 10 --fps 60
+
+# Shared cache across pipelines, forcing recomputation
+jabs-cli compute-features --pose-file session_pose_est_v6.h5 --feature-dir /shared/features \
+    --use-pose-hash --force
+```
+
 ## jabs-cli update-pose
 
 The `jabs-cli update-pose` command updates an existing JABS project to use updated pose files for the same videos while remapping existing labels onto the updated poses. This is intended for keeping labels when pose files have been regenerated or otherwise updated.
@@ -250,6 +275,35 @@ jabs-cli update-labels /path/to/target_project /path/to/source_project --min-iou
 
 If instead you want to replace the target's pose while keeping its labels, see [`jabs-cli update-pose`](#jabs-cli-update-pose).
 
+## jabs-cli merge
+
+The `jabs-cli merge` command merges a source JABS project into a destination JABS project. Videos, pose files, behaviors, and labels from the source project are imported into the destination project, which is modified in place. The source project is left unchanged.
+
+Note: this command was previously the standalone `jabs-project-merge` script, which has been removed.
+
+**Usage:**
+
+```bash
+jabs-cli merge <destination_project> <source_project> --merge-strategy <STRATEGY>
+```
+
+- `<destination_project>`: Path to the destination JABS project. This project is modified by importing videos and labels from the source project.
+- `<source_project>`: Path to the source JABS project. Not modified.
+- `--merge-strategy <STRATEGY>`: Required. How to resolve conflicting labels, i.e. frames labeled differently in both projects for the same video, identity, and behavior:
+    - `behavior-wins`: Keep the label with the behavior annotation.
+    - `not-behavior-wins`: Keep the label without the behavior annotation.
+    - `destination-wins`: Keep the label from the destination project.
+
+Videos present only in the source project are copied into the destination project along with their pose files, and behaviors defined only in the source project are added to the destination project's `project.json`. Labels for videos already in the destination project are merged annotation by annotation using the selected strategy.
+
+Both paths must already be valid JABS project directories, and they must be different directories.
+
+**Example:**
+
+```bash
+jabs-cli merge /path/to/destination_project /path/to/source_project --merge-strategy destination-wins
+```
+
 ## jabs-cli sample-frames
 
 The `jabs-cli sample-frames` command extracts individual video frames as PNG images
diff --git a/src/jabs/scripts/cli/cli.py b/src/jabs/scripts/cli/cli.py
index 69a10b44..eecc6616 100644
--- a/src/jabs/scripts/cli/cli.py
+++ b/src/jabs/scripts/cli/cli.py
@@ -26,6 +26,7 @@
 from .convert_parquet import convert_parquet_command
 from .convert_to_nwb import run_conversion
 from .cross_validation import run_cross_validation
+from .merge_projects import merge_projects_command
 from .postprocessing import apply_postprocessing_command
 from .sample_frames import sample_frames_command
 from .sample_pose_intervals import sample_pose_intervals_command
@@ -53,6 +54,7 @@ def cli(ctx: click.Context, verbose):
 cli.add_command(apply_postprocessing_command)
 cli.add_command(compute_features_command)
 cli.add_command(convert_parquet_command)
+cli.add_command(merge_projects_command)
 cli.add_command(update_pose_command)
 cli.add_command(update_labels_command)
 cli.add_command(sample_pose_intervals_command)
diff --git a/src/jabs/scripts/cli/merge_projects.py b/src/jabs/scripts/cli/merge_projects.py
new file mode 100644
index 00000000..4831784b
--- /dev/null
+++ b/src/jabs/scripts/cli/merge_projects.py
@@ -0,0 +1,77 @@
+"""Merge one JABS project into another.
+
+The source project's videos, pose files, behaviors, and labels are imported into
+the destination project, which is modified in place. The source project is left
+unchanged.
+
+Where both projects label the same video, identity, and behavior, conflicting
+labels are resolved by the selected ``--merge-strategy``:
+
+\b
+  * behavior-wins:      Keep the label with the behavior annotation.
+  * not-behavior-wins:  Keep the label without the behavior annotation.
+  * destination-wins:   Keep the label from the destination project.
+
+Example:
+
+\b
+  jabs-cli merge /path/to/destination_project /path/to/source_project --merge-strategy destination-wins
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import click
+
+from jabs.project import Project
+from jabs.project.project_merge import MergeStrategy, merge_projects
+
+MERGE_STRATEGY_MAP: dict[str, MergeStrategy] = {
+    "behavior-wins": MergeStrategy.BEHAVIOR_WINS,
+    "not-behavior-wins": MergeStrategy.NOT_BEHAVIOR_WINS,
+    "destination-wins": MergeStrategy.DESTINATION_WINS,
+}
+
+
+@click.command(
+    name="merge",
+    context_settings={"max_content_width": 120},
+    help=__doc__,
+)
+@click.argument(
+    "destination_project",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+)
+@click.argument(
+    "source_project",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+)
+@click.option(
+    "--merge-strategy",
+    "merge_strategy",
+    type=click.Choice(list(MERGE_STRATEGY_MAP), case_sensitive=False),
+    required=True,
+    help="Strategy to use when merging conflicting labels.",
+)
+def merge_projects_command(
+    destination_project: Path,
+    source_project: Path,
+    merge_strategy: str,
+) -> None:
+    """Merge a source JABS project into a destination JABS project."""
+    if destination_project.resolve() == source_project.resolve():
+        raise click.ClickException("Destination and source projects cannot be the same.")
+
+    if not Project.is_valid_project_directory(destination_project):
+        raise click.ClickException(
+            f"Destination project {destination_project} is not a valid JABS project."
+        )
+
+    if not Project.is_valid_project_directory(source_project):
+        raise click.ClickException(f"Source project {source_project} is not a valid JABS project.")
+
+    destination = Project(destination_project)
+    source = Project(source_project)
+
+    merge_projects(destination, source, MERGE_STRATEGY_MAP[merge_strategy.lower()])
diff --git a/src/jabs/scripts/generate_features.py b/src/jabs/scripts/generate_features.py
index be27f0e8..61ae49a7 100644
--- a/src/jabs/scripts/generate_features.py
+++ b/src/jabs/scripts/generate_features.py
@@ -1,70 +1,71 @@
 #!/usr/bin/env python
 
-"""initialize JABS features for a pose file
+"""Deprecated entry point for computing JABS features for a pose file.
 
-computes features if they do not exist
+``jabs-features`` has been replaced by ``jabs-cli compute-features``. This module
+is kept only as a transitional shim: it accepts the legacy argument surface,
+prints a deprecation warning, translates the legacy options to their
+``compute-features`` equivalents, and then runs that command.
+
+Legacy option mapping:
+
+* ``--pose-version`` is ignored. ``compute-features`` infers the pose version
+  from the pose filename (e.g. ``*_pose_est_v6.h5``).
+* ``--use-cm-distances`` selects cm units, which is the ``compute-features``
+  default when the pose file provides a pixel-to-cm scale. Without the flag,
+  ``--use-pixel-distances`` is forwarded to preserve the legacy pixel default.
+* ``--window-size`` maps to a single ``-w`` value.
+* ``--fps`` and ``--use-pose-hash`` are forwarded unchanged.
+
+The feature cache is always written in Parquet format, which is also the
+``compute-features`` default.
 """
 
 import argparse
 import sys
 from pathlib import Path
 
-from jabs.core.enums import CacheFormat, ProjectDistanceUnit
-from jabs.feature_extraction.features import IdentityFeatures
-from jabs.pose_estimation import open_pose_file
-from jabs.project import Project
+from .cli.compute_features import compute_features_command
 
 
-def generate_feature_cache(args):
-    """
-    Generate and cache features for each identity in a pose file.
+def _build_compute_features_args(args: argparse.Namespace) -> list[str]:
+    """Translate legacy ``jabs-features`` arguments into ``compute-features`` arguments."""
+    command_args = [
+        "--pose-file",
+        str(args.pose_file),
+        "--feature-dir",
+        str(args.feature_dir),
+        "--fps",
+        str(args.fps),
+    ]
 
-    Loads the pose file, computes features for each identity using the specified
-    settings, and caches the results in the given feature directory. Optionally
-    generates window features if a window size is provided.
+    # the legacy script defaulted to pixel units and opted into cm; compute-features
+    # defaults to cm when the pose file has a pixel-to-cm scale and opts into pixel
+    if not args.cm_units:
+        command_args.append("--use-pixel-distances")
 
-    Args:
-        args: argparse Namespace object containing script arguments, including pose file path,
-              pose version, feature directory, distance unit, window size, and fps.
-    """
-    distance_unit = ProjectDistanceUnit.CM if args.cm_units else ProjectDistanceUnit.PIXEL
-    settings = Project.settings_by_pose_version(args.pose_version, distance_unit)
     if args.window_size is not None:
-        settings["window_size"] = args.window_size
-        cache_window = True
-    else:
-        cache_window = False
-
-    pose_est = open_pose_file(args.pose_file)
-    for curr_id in pose_est.identities:
-        # Note: Features are still cached with the highest pose version.
-        # It isn't until get_features is called that filtering occurs
-        features = IdentityFeatures(
-            args.pose_file,
-            curr_id,
-            args.feature_dir,
-            pose_est,
-            fps=args.fps,
-            op_settings=settings,
-            cache_window=cache_window,
-            cache_format=CacheFormat.PARQUET,
-            include_pose_hash=args.use_pose_hash,
-        )
-        # Window features are not automatically generated.
-        if cache_window:
-            _ = features.get_window_features(
-                settings["window_size"], settings["social"], force=True
-            )
+        command_args += ["-w", str(args.window_size)]
+
+    if args.use_pose_hash:
+        command_args.append("--use-pose-hash")
+
+    return command_args
 
 
 def main():
-    """jabs-features"""
+    """jabs-features (deprecated): forward to ``jabs-cli compute-features``."""
     script = Path(sys.argv[0]).name
     print(
         f"{script} is deprecated, use `jabs-cli compute-features` instead.",
         file=sys.stderr,
     )
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(
+        description=(
+            f"DEPRECATED: {script} forwards to `jabs-cli compute-features`. "
+            "Use that command directly."
+        )
+    )
     parser.add_argument(
         "--pose-file",
         required=True,
@@ -73,9 +74,9 @@ def main():
     )
     parser.add_argument(
         "--pose-version",
-        required=True,
         type=int,
-        help="pose version to calculate features",
+        default=None,
+        help="ignored, the pose version is inferred from the pose filename",
     )
     parser.add_argument(
         "--feature-dir",
@@ -97,7 +98,7 @@ def main():
         help="window size for features (default none)",
     )
     parser.add_argument(
-        "--fps", default=30, help="frames per second to use for feature calculation"
+        "--fps", type=int, default=30, help="frames per second to use for feature calculation"
     )
     parser.add_argument(
         "--use-pose-hash",
@@ -112,7 +113,16 @@ def main():
     )
     args = parser.parse_args()
 
-    generate_feature_cache(args)
+    if args.pose_version is not None:
+        print(
+            "--pose-version is ignored, the pose version is inferred from the pose filename.",
+            file=sys.stderr,
+        )
+
+    compute_features_command.main(
+        _build_compute_features_args(args),
+        prog_name="jabs-cli compute-features",
+    )
 
 
 if __name__ == "__main__":
diff --git a/src/jabs/scripts/merge_projects.py b/src/jabs/scripts/merge_projects.py
deleted file mode 100644
index 638c1bd0..00000000
--- a/src/jabs/scripts/merge_projects.py
+++ /dev/null
@@ -1,87 +0,0 @@
-import argparse
-import sys
-from pathlib import Path
-
-from rich.console import Console
-from rich.markdown import Markdown
-from rich_argparse import RichHelpFormatter
-
-from jabs.project import Project
-from jabs.project.project_merge import MergeStrategy, merge_projects
-
-MERGE_STRATEGY_MAP: dict[str, tuple[MergeStrategy, str]] = {
-    "behavior-wins": (MergeStrategy.BEHAVIOR_WINS, "Keep the label with the behavior annotation."),
-    "not-behavior-wins": (
-        MergeStrategy.NOT_BEHAVIOR_WINS,
-        "Keep the label without the behavior annotation.",
-    ),
-    "destination-wins": (
-        MergeStrategy.DESTINATION_WINS,
-        "Keep the label from the destination project.",
-    ),
-}
-
-max_key_len = max(len(key) for key in MERGE_STRATEGY_MAP)
-MERGE_STRATEGY_DETAILS = "About Merge Strategy Options:\n" + "\n".join(
-    f"  * {(key + ':').ljust(max_key_len + 1)}  {desc}"
-    for key, (_, desc) in MERGE_STRATEGY_MAP.items()
-)
-
-
-def rich_error_exit(message: str) -> None:
-    """Print a formatted error message and exit the program."""
-    console = Console()
-    console.print(f"\n  [bold red]ERROR:[/bold red] {message}\n")
-    sys.exit(1)
-
-
-def main():
-    """project merge script entry point."""
-
-    def dir_path(path_str: str) -> Path:
-        path = Path(path_str)
-        if not path.is_dir():
-            raise argparse.ArgumentTypeError(f"{path} is not a valid directory")
-        return path
-
-    """Command for merging two JABS projects."""
-    parser = argparse.ArgumentParser(
-        description="Merge two JABS projects.",
-        epilog=Markdown(MERGE_STRATEGY_DETAILS, style="argparse.text"),  # type: ignore
-        formatter_class=RichHelpFormatter,
-    )
-    parser.add_argument(
-        "destination_project",
-        type=dir_path,
-        help="Path to the destination project. This project will be modified by importing videos and labels from the"
-        " source project.",
-    )
-    parser.add_argument("source_project", type=dir_path, help="Path to the source project.")
-    parser.add_argument(
-        "--merge-strategy",
-        choices=MERGE_STRATEGY_MAP.keys(),
-        required=True,
-        default="destination-wins",
-        help="Strategy to use when merging conflicting labels. (default: destination-wins)",
-    )
-    args = parser.parse_args()
-
-    if args.destination_project == args.source_project:
-        rich_error_exit("Destination and source projects cannot be the same.")
-
-    if not (args.destination_project / "jabs").exists():
-        rich_error_exit(
-            f"Destination project {args.destination_project} is not a valid JABS project."
-        )
-
-    if not (args.source_project / "jabs").exists():
-        rich_error_exit(f"Source project {args.source_project} is not a valid JABS project.")
-
-    destination = Project(args.destination_project)
-    source = Project(args.source_project)
-
-    merge_projects(destination, source, MERGE_STRATEGY_MAP[args.merge_strategy][0])
-
-
-if __name__ == "__main__":
-    main()
diff --git a/src/jabs/ui/dialogs/user_guide_dialog.py b/src/jabs/ui/dialogs/user_guide_dialog.py
index 408dfbc4..025d98ad 100644
--- a/src/jabs/ui/dialogs/user_guide_dialog.py
+++ b/src/jabs/ui/dialogs/user_guide_dialog.py
@@ -195,11 +195,12 @@ def _build_tree(self) -> None:
             "Command Line Tools": {
                 "_file": "cli-tools.md",
                 "jabs-classify": "cli-tools.md#jabs-classify",
-                "jabs-features": "cli-tools.md#jabs-features",
                 "jabs-cli": {
                     "_file": "cli-tools.md#jabs-cli",
+                    "compute-features": "cli-tools.md#jabs-cli-compute-features",
                     "update-pose": "cli-tools.md#jabs-cli-update-pose",
                     "update-labels": "cli-tools.md#jabs-cli-update-labels",
+                    "merge": "cli-tools.md#jabs-cli-merge",
                 },
                 "jabs-init": "cli-tools.md#jabs-init",
             },
diff --git a/tests/scripts/test_generate_features.py b/tests/scripts/test_generate_features.py
new file mode 100644
index 00000000..11b6b3d1
--- /dev/null
+++ b/tests/scripts/test_generate_features.py
@@ -0,0 +1,147 @@
+"""Tests for the deprecated ``jabs-features`` shim."""
+
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+from jabs.scripts import generate_features
+
+MODULE = "jabs.scripts.generate_features"
+
+
+def _legacy_args(**overrides) -> argparse.Namespace:
+    """Build a legacy argparse namespace with sensible defaults."""
+    defaults = {
+        "pose_file": Path("session_pose_est_v6.h5"),
+        "pose_version": None,
+        "feature_dir": Path("features"),
+        "cm_units": False,
+        "window_size": None,
+        "fps": 30,
+        "use_pose_hash": False,
+    }
+    defaults.update(overrides)
+    return argparse.Namespace(**defaults)
+
+
+def test_translation_defaults_to_pixel_distances() -> None:
+    """Without --use-cm-distances the legacy pixel default is preserved."""
+    result = generate_features._build_compute_features_args(_legacy_args())
+
+    assert result == [
+        "--pose-file",
+        "session_pose_est_v6.h5",
+        "--feature-dir",
+        "features",
+        "--fps",
+        "30",
+        "--use-pixel-distances",
+    ]
+
+
+def test_translation_cm_distances_omits_pixel_flag() -> None:
+    """--use-cm-distances leaves compute-features on its cm-when-available default."""
+    result = generate_features._build_compute_features_args(_legacy_args(cm_units=True))
+
+    assert "--use-pixel-distances" not in result
+
+
+def test_translation_forwards_window_size_fps_and_pose_hash() -> None:
+    """Legacy window size, fps, and pose hash options map onto the new command."""
+    result = generate_features._build_compute_features_args(
+        _legacy_args(window_size=5, fps=60, use_pose_hash=True)
+    )
+
+    assert result[result.index("-w") + 1] == "5"
+    assert result[result.index("--fps") + 1] == "60"
+    assert "--use-pose-hash" in result
+
+
+def test_translation_drops_pose_version() -> None:
+    """--pose-version is not forwarded, the new command infers it from the filename."""
+    result = generate_features._build_compute_features_args(_legacy_args(pose_version=3))
+
+    assert "--pose-version" not in result
+
+
+def test_main_prints_deprecation_and_runs_command(
+    monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture[str], tmp_path: Path
+) -> None:
+    """The shim warns on stderr and then invokes compute-features."""
+    pose_file = tmp_path / "session_pose_est_v6.h5"
+    pose_file.touch()
+    feature_dir = tmp_path / "features"
+
+    monkeypatch.setattr(
+        "sys.argv",
+        [
+            "jabs-features",
+            "--pose-file",
+            str(pose_file),
+            "--feature-dir",
+            str(feature_dir),
+            "--window-size",
+            "5",
+        ],
+    )
+    with mock.patch(f"{MODULE}.compute_features_command") as mock_command:
+        generate_features.main()
+
+    captured = capsys.readouterr()
+    assert "jabs-features is deprecated" in captured.err
+    assert "jabs-cli compute-features" in captured.err
+
+    mock_command.main.assert_called_once()
+    forwarded = mock_command.main.call_args.args[0]
+    assert forwarded == [
+        "--pose-file",
+        str(pose_file),
+        "--feature-dir",
+        str(feature_dir),
+        "--fps",
+        "30",
+        "--use-pixel-distances",
+        "-w",
+        "5",
+    ]
+
+
+def test_main_warns_that_pose_version_is_ignored(
+    monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture[str], tmp_path: Path
+) -> None:
+    """Passing the legacy --pose-version produces a warning and is not forwarded."""
+    pose_file = tmp_path / "session_pose_est_v6.h5"
+    pose_file.touch()
+
+    monkeypatch.setattr(
+        "sys.argv",
+        [
+            "jabs-features",
+            "--pose-file",
+            str(pose_file),
+            "--pose-version",
+            "3",
+            "--feature-dir",
+            str(tmp_path / "features"),
+        ],
+    )
+    with mock.patch(f"{MODULE}.compute_features_command") as mock_command:
+        generate_features.main()
+
+    captured = capsys.readouterr()
+    assert "--pose-version is ignored" in captured.err
+    assert "--pose-version" not in mock_command.main.call_args.args[0]
+
+
+def test_main_still_requires_pose_file_and_feature_dir(monkeypatch: pytest.MonkeyPatch) -> None:
+    """The legacy required options are still enforced by the shim."""
+    monkeypatch.setattr("sys.argv", ["jabs-features", "--pose-file", "session_pose_est_v6.h5"])
+
+    with pytest.raises(SystemExit) as exc_info:
+        generate_features.main()
+
+    assert exc_info.value.code != 0
diff --git a/tests/scripts/test_merge_projects_cli.py b/tests/scripts/test_merge_projects_cli.py
new file mode 100644
index 00000000..ffbe3ea4
--- /dev/null
+++ b/tests/scripts/test_merge_projects_cli.py
@@ -0,0 +1,121 @@
+"""Tests for the ``jabs-cli merge`` subcommand."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from unittest import mock
+
+from click.testing import CliRunner
+
+from jabs.project.project_merge import MergeStrategy
+from jabs.scripts.cli.cli import cli
+
+
+def _make_project_dir(path: Path) -> Path:
+    """Create a directory that passes ``Project.is_valid_project_directory``."""
+    (path / "jabs").mkdir(parents=True)
+    (path / "jabs" / "project.json").write_text("{}")
+    return path
+
+
+def test_merge_strategy_is_required(tmp_path: Path) -> None:
+    """Omitting --merge-strategy is an error."""
+    dest = _make_project_dir(tmp_path / "dest")
+    source = _make_project_dir(tmp_path / "source")
+
+    result = CliRunner().invoke(cli, ["merge", str(dest), str(source)])
+
+    assert result.exit_code != 0
+    assert "--merge-strategy" in result.output
+
+
+def test_same_project_rejected(tmp_path: Path) -> None:
+    """Merging a project into itself is rejected before any project is opened."""
+    project = _make_project_dir(tmp_path / "project")
+
+    with mock.patch("jabs.scripts.cli.merge_projects.Project") as mock_project:
+        result = CliRunner().invoke(
+            cli,
+            ["merge", str(project), str(project), "--merge-strategy", "destination-wins"],
+        )
+
+    assert result.exit_code != 0
+    assert "cannot be the same" in result.output
+    mock_project.assert_not_called()
+
+
+def test_invalid_destination_project_rejected(tmp_path: Path) -> None:
+    """A destination directory that is not a JABS project is rejected."""
+    dest = tmp_path / "dest"
+    dest.mkdir()
+    source = _make_project_dir(tmp_path / "source")
+
+    result = CliRunner().invoke(
+        cli,
+        ["merge", str(dest), str(source), "--merge-strategy", "destination-wins"],
+    )
+
+    assert result.exit_code != 0
+    assert "Destination project" in result.output
+    assert "not a valid JABS project" in result.output
+
+
+def test_invalid_source_project_rejected(tmp_path: Path) -> None:
+    """A source directory that is not a JABS project is rejected."""
+    dest = _make_project_dir(tmp_path / "dest")
+    source = tmp_path / "source"
+    source.mkdir()
+
+    result = CliRunner().invoke(
+        cli,
+        ["merge", str(dest), str(source), "--merge-strategy", "destination-wins"],
+    )
+
+    assert result.exit_code != 0
+    assert "Source project" in result.output
+    assert "not a valid JABS project" in result.output
+
+
+def test_missing_project_directory_rejected(tmp_path: Path) -> None:
+    """A nonexistent project path fails click's path validation."""
+    dest = _make_project_dir(tmp_path / "dest")
+    missing = tmp_path / "does_not_exist"
+
+    result = CliRunner().invoke(
+        cli,
+        ["merge", str(dest), str(missing), "--merge-strategy", "destination-wins"],
+    )
+
+    assert result.exit_code != 0
+    assert "does_not_exist" in result.output
+
+
+def test_merge_invoked_with_selected_strategy(tmp_path: Path) -> None:
+    """Valid inputs open both projects and forward the selected merge strategy."""
+    dest = _make_project_dir(tmp_path / "dest")
+    source = _make_project_dir(tmp_path / "source")
+
+    # distinct instances so the assertion below fails if the same project is
+    # forwarded twice, or if only one of the two is ever instantiated
+    dest_project = mock.Mock(name="destination_project")
+    source_project = mock.Mock(name="source_project")
+
+    with (
+        mock.patch(
+            "jabs.scripts.cli.merge_projects.Project",
+            side_effect=[dest_project, source_project],
+        ) as mock_project,
+        mock.patch("jabs.scripts.cli.merge_projects.merge_projects") as mock_merge,
+    ):
+        result = CliRunner().invoke(
+            cli,
+            ["merge", str(dest), str(source), "--merge-strategy", "behavior-wins"],
+        )
+
+    assert result.exit_code == 0, result.output
+    assert mock_project.call_args_list == [mock.call(dest), mock.call(source)]
+    mock_merge.assert_called_once_with(
+        dest_project,
+        source_project,
+        MergeStrategy.BEHAVIOR_WINS,
+    )
diff --git a/uv.lock b/uv.lock
index ba5668fb..c1a885f0 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1801,7 +1801,6 @@ dependencies = [
     { name = "pyside6" },
     { name = "qt-material-icons" },
     { name = "rich" },
-    { name = "rich-argparse" },
     { name = "scikit-learn", version = "1.7.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
     { name = "scikit-learn", version = "1.8.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
     { name = "shapely" },
@@ -1865,7 +1864,6 @@ requires-dist = [
     { name = "pyyaml", marker = "extra == 'yaml'", specifier = ">=6.0.0" },
     { name = "qt-material-icons", specifier = ">=0.2.0,<0.3.0" },
     { name = "rich", specifier = ">=14.0.0,<15.0.0" },
-    { name = "rich-argparse", specifier = ">=1.7.1,<2.0.0" },
     { name = "scikit-learn", specifier = ">=1.5.0,<2.0.0" },
     { name = "shapely", specifier = ">=2.0.1,<3.0.0" },
     { name = "tabulate", specifier = ">=0.9.0,<1.0.0" },
@@ -4211,18 +4209,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/b3/76/6d163cfac87b632216f71879e6b2cf17163f773ff59c00b5ff4900a80fa3/rich-14.3.4-py3-none-any.whl", hash = "sha256:07e7adb4690f68864777b1450859253bed81a99a31ac321ac1817b2313558952", size = 310480, upload-time = "2026-04-11T02:57:47.484Z" },
 ]
 
-[[package]]
-name = "rich-argparse"
-version = "1.7.2"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "rich" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/4c/f7/1c65e0245d4c7009a87ac92908294a66e7e7635eccf76a68550f40c6df80/rich_argparse-1.7.2.tar.gz", hash = "sha256:64fd2e948fc96e8a1a06e0e72c111c2ce7f3af74126d75c0f5f63926e7289cd1", size = 38500, upload-time = "2025-11-01T10:35:44.232Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/04/80/97b6f357ac458d9ad9872cc3183ca09ef7439ac89e030ea43053ba1294b6/rich_argparse-1.7.2-py3-none-any.whl", hash = "sha256:0559b1f47a19bbeb82bf15f95a057f99bcbbc98385532f57937f9fc57acc501a", size = 25476, upload-time = "2025-11-01T10:35:42.681Z" },
-]
-
 [[package]]
 name = "rpds-py"
 version = "0.30.0"