fix: more fixes/improvements (MODFLOW-ORG#283)

* add commands for models and programs CLIs, with root mf namespace
* add : interactive bindir prompt like flopy's get-modflow, with similar options
* fix exe path resolution

Author: wpbonelli

docs/md/dev/models.md

@@ -337,36 +337,36 @@ The simplest approach would be a single such script/command, e.g. `python -m mod
 
 ```bash
 # Show configured registries and status
-python -m modflow_devtools.models info
+mf models info
 
 # Sync all sources to configured refs
-python -m modflow_devtools.models sync
+mf models sync
 
 # Force re-download even if cached
-python -m modflow_devtools.models sync --force
+mf models sync --force
 
 # For a repo publishing models via releases
-python -m modflow_devtools.models sync --repo MODFLOW-ORG/modflow6-examples --ref current
+mf models sync --repo MODFLOW-ORG/modflow6-examples --ref current
 
 # For a repo with models under version control
-python -m modflow_devtools.models sync --repo MODFLOW-ORG/modflow6-testmodels --ref develop 
-python -m modflow_devtools.models sync --repo MODFLOW-ORG/modflow6-testmodels --ref f3df630  # commit hash works too
-```
-
-Or via CLI commands:
-
-```bash
-models info
-models sync
+mf models sync --repo MODFLOW-ORG/modflow6-testmodels --ref develop
+mf models sync --repo MODFLOW-ORG/modflow6-testmodels --ref f3df630  # commit hash works too
 ```
 
-Perhaps leading with a `models` command namespace is too generic, and we need e.g. a leading `mf` namespace on all commands exposed by `modflow-devtools`:
+CLI commands are available in two forms:
 
 ```bash
+# Using the mf namespace (shorter)
 mf models info
 mf models sync
+
+# Or using the module form
+python -m modflow_devtools.models info
+python -m modflow_devtools.models sync
 ```
 
+The `mf` command provides a unified CLI namespace for all `modflow-devtools` commands.
+
 #### Automatic sync
 
 At install time, `modflow-devtools` can load the bootstrap file and attempt to sync to all configured repositories/registries. The install should not fail if registry sync fails (due either to network errors or misconfiguration), however — an informative warning can be shown, and sync retried on subsequent imports and/or manually (see below).
@@ -709,7 +709,7 @@ _DEFAULT_CACHE.clear()
 #### Show Registry Status
 
 ```bash
-$ python -m modflow_devtools.models info
+$ mf models info
 
 Registry sync status:
 
@@ -727,19 +727,19 @@ mf6/example (MODFLOW-ORG/modflow6-examples)
 
 ```bash
 # Sync all configured sources/refs
-$ python -m modflow_devtools.models sync
+$ mf models sync
 
 # Sync specific source
-$ python -m modflow_devtools.models sync --source modflow6-testmodels
+$ mf models sync --source modflow6-testmodels
 
 # Sync specific ref
-$ python -m modflow_devtools.models sync --source modflow6-testmodels --ref develop
+$ mf models sync --source modflow6-testmodels --ref develop
 
 # Force re-download
-$ python -m modflow_devtools.models sync --force
+$ mf models sync --force
 
 # Test against a fork
-$ python -m modflow_devtools.models sync \
+$ mf models sync \
     --source modflow6-testmodels \
     --ref feature-branch \
     --repo myusername/modflow6-testmodels
@@ -749,19 +749,19 @@ $ python -m modflow_devtools.models sync \
 
 ```bash
 # Summary view
-$ python -m modflow_devtools.models list
+$ mf models list
 
 # Verbose view (show all model names)
-$ python -m modflow_devtools.models list --verbose
+$ mf models list --verbose
 
 # Filter by source
-$ python -m modflow_devtools.models list --source mf6/test
+$ mf models list --source mf6/test
 
 # Filter by ref
-$ python -m modflow_devtools.models list --ref registry
+$ mf models list --ref registry
 
 # Combine filters
-$ python -m modflow_devtools.models list --source mf6/test --ref registry --verbose
+$ mf models list --source mf6/test --ref registry --verbose
 ```
 
 ### Registry Creation Tool

docs/md/dev/programs.md

@@ -481,19 +481,19 @@ Exposed as a CLI command and Python API:
 
 ```bash
 # Sync all configured sources and release tags
-python -m modflow_devtools.programs sync
+mf programs sync
 
-# Sync specific source to specific release version
-python -m modflow_devtools.programs sync --repo MODFLOW-ORG/modflow6 --version 6.6.3
+# Sync specific source
+mf programs sync --source modflow6
 
 # Force re-download
-python -m modflow_devtools.programs sync --force
+mf programs sync --force
 
 # Show sync status
-python -m modflow_devtools.programs info
+mf programs info
 
 # List available programs
-python -m modflow_devtools.programs list
+mf programs list
 ```
 
 Or via Python API:
@@ -544,15 +544,15 @@ The `--force` flag has different meanings depending on the command, maintaining
 **Common patterns**:
 ```bash
 # Update to latest registry and install
-python -m modflow_devtools.programs sync --force
-python -m modflow_devtools.programs install mf6
+mf programs sync --force
+mf programs install mf6
 
 # Repair installation without touching registry (offline-friendly)
-python -m modflow_devtools.programs install mf6 --force
+mf programs install mf6 --force
 
 # Complete refresh of both metadata and installation
-python -m modflow_devtools.programs sync --force
-python -m modflow_devtools.programs install mf6 --force
+mf programs sync --force
+mf programs install mf6 --force
 ```
 
 ### Program installation
@@ -561,38 +561,27 @@ Installation extends beyond metadata to actually providing program executables b
 
 ```bash
 # Install from binary (auto-detects platform)
-python -m modflow_devtools.programs install mf6
+mf programs install mf6
 
 # Install specific version
-python -m modflow_devtools.programs install mf6@6.6.3
+mf programs install mf6@6.6.3
 
-# Install to custom location (interactive selection like get-modflow)
-python -m modflow_devtools.programs install mf6 --bindir :
-
-# Install to specific directory
-python -m modflow_devtools.programs install mf6 --bindir /usr/local/bin
+# Install to custom location
+mf programs install mf6 --bindir /usr/local/bin
 
 # Install multiple versions side-by-side (cached separately)
-python -m modflow_devtools.programs install mf6@6.6.3
-python -m modflow_devtools.programs install mf6@6.5.0
-
-# Select active version (re-copies from cache to bindir)
-python -m modflow_devtools.programs select mf6@6.6.3
-
-# List installed programs
-python -m modflow_devtools.programs list --installed
-
-# List available versions of a program
-python -m modflow_devtools.programs list mf6
+mf programs install mf6@6.6.3
+mf programs install mf6@6.5.0
 
-# Show where program is installed
-python -m modflow_devtools.programs which mf6
+# List installation history
+mf programs history
+mf programs history mf6
 
 # Uninstall specific version
-python -m modflow_devtools.programs uninstall mf6@6.6.3
+mf programs uninstall mf6@6.6.3
 
 # Uninstall all versions
-python -m modflow_devtools.programs uninstall mf6 --all
+mf programs uninstall mf6 --all
 ```
 
 Python API:
@@ -1055,14 +1044,14 @@ The Programs API has been implemented following a consolidated object-oriented a
 - Force re-download support
 
 **CLI Interface** ✅
-- `python -m modflow_devtools.programs sync` - Sync registries
-- `python -m modflow_devtools.programs info` - Show sync status
-- `python -m modflow_devtools.programs list` - List available programs
-- `python -m modflow_devtools.programs install` - Install a program
-- `python -m modflow_devtools.programs select` - Switch active version
-- `python -m modflow_devtools.programs uninstall` - Uninstall a program
-- `python -m modflow_devtools.programs which` - Show executable path
-- `python -m modflow_devtools.programs installed` - List installed programs
+- `mf programs sync` - Sync registries
+- `mf programs info` - Show sync status
+- `mf programs list` - List available programs
+- `mf programs install` - Install a program
+- `mf programs uninstall` - Uninstall a program
+- `mf programs history` - Show installation history
+
+All commands also support the module form: `python -m modflow_devtools.programs <command>`
 
 **Registry Generation Tool** ✅
 - `modflow_devtools/programs/make_registry.py` - Generate registry files

docs/md/models.md

@@ -77,9 +77,16 @@ for source_name, source_status in status.items():
     print(f"{source_name}: {source_status.cached_refs}")
 ```
 
-Or via CLI:
+Or via CLI (both forms are equivalent):
 
 ```bash
+# Using the mf command
+mf models sync
+mf models sync --source modflow6-testmodels
+mf models sync --source modflow6-testmodels --ref develop
+mf models sync --force
+
+# Or using the module form
 python -m modflow_devtools.models sync
 python -m modflow_devtools.models sync --source modflow6-testmodels
 python -m modflow_devtools.models sync --source modflow6-testmodels --ref develop
@@ -101,10 +108,17 @@ for example_name, model_list in list(examples.items())[:3]:
     print(f"{example_name}: {len(model_list)} models")
 ```
 
-Or by CLI:
+Or by CLI (both forms are equivalent):
 
 ```bash
+# Using the mf command
+mf models info  # Show sync status
+mf models list  # Show model summary...
+mf models list --verbose  # ..or full list
+# Filter by source
+mf models list --source mf6/test --verbose
 
+# Or using the module form
 python -m modflow_devtools.models info  # Show sync status
 python -m modflow_devtools.models list  # Show model summary...
 python -m modflow_devtools.models list --verbose  # ..or full list
@@ -268,7 +282,8 @@ export MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1
 Then manually sync when needed:
 
 ```bash
-python -m modflow_devtools.models sync
+mf models sync
+# Or: python -m modflow_devtools.models sync
 ```
 
 ## Repository Integration