Code cleanup

Author: daniel-thom

docs/src/core/how-to/cancel-workflow.md

@@ -45,9 +45,10 @@ To resume a canceled workflow:
 # Reinitialize to reset canceled jobs
 torc reinit <workflow_id>
 
-# Run again
-torc workflows run <workflow_id>
-torc workflows submit <workflow_id>
+# Run again locally
+torc run <workflow_id>
+# Or submit to scheduler
+torc submit <workflow_id>
 ```
 
 Jobs that completed before cancellation remain completed.

docs/src/core/how-to/debug-failed-job.md

@@ -92,9 +92,10 @@ After fixing the issue:
 # Reinitialize to reset failed jobs
 torc workflows reset-status --failed --reinitialize <workflow_id>
 
-# Run again
-torc workflows run <workflow_id>
-torc slurm generate <workflow_id> && torc submit <workflow_id>
+# Run again locally
+torc run <workflow_id>
+# Or re-submit to Slurm
+torc submit <workflow_id>
 ```
 
 ## See Also

docs/src/core/reference/cli.md

@@ -135,24 +135,14 @@ torc slurm generate --account <account> -o workflow_with_schedulers.yaml workflo
 torc submit workflow_with_schedulers.yaml
 ```
 
-**Usage:** `torc submit-slurm [OPTIONS] --account <ACCOUNT> <WORKFLOW_SPEC>`
+**Usage:**
 
-###### **Arguments:**
-
-- `<WORKFLOW_SPEC>` — Path to workflow spec file (JSON/JSON5/YAML/KDL)
-
-###### **Options:**
+```bash
+torc slurm generate [OPTIONS] --account <ACCOUNT> <WORKFLOW_FILE>
+torc submit <OUTPUT_FILE>
+```
 
-- `--account <ACCOUNT>` — Slurm account to use for allocations
-- `--hpc-profile <HPC_PROFILE>` — HPC profile to use (auto-detected if not specified)
-- `--single-allocation` — Bundle all nodes into a single Slurm allocation per scheduler. By default,
-  creates one Slurm allocation per node (N×1 mode), which allows jobs to start as nodes become
-  available and provides better fault tolerance. With this flag, creates one large allocation with
-  all nodes (1×N mode), which requires all nodes to be available simultaneously but uses a single
-  sbatch.
-- `-i`, `--ignore-missing-data` — Ignore missing data. Default: `false`
-- `--skip-checks` — Skip validation checks (e.g., scheduler node requirements). Use with caution.
-  Default: `false`
+See [`torc slurm generate`](#torc-slurm-generate) for full options.
 
 ## `torc watch`
 
@@ -523,39 +513,6 @@ Archive or unarchive one or more workflows
 - `<IS_ARCHIVED>` — Set to true to archive, false to unarchive
 - `<WORKFLOW_IDS>` — IDs of workflows to archive/unarchive (if empty, will prompt for selection)
 
-## `torc workflows submit`
-
-Submit a workflow: initialize if needed and schedule nodes for on_workflow_start actions. This
-command requires the workflow to have an on_workflow_start action with schedule_nodes.
-
-**Usage:** `torc workflows submit [OPTIONS] [WORKFLOW_ID]`
-
-###### **Arguments:**
-
-- `<WORKFLOW_ID>` — ID of the workflow to submit (optional - will prompt if not provided)
-
-###### **Options:**
-
-- `--force` — If false, fail the operation if missing data is present. Default: `false`
-
-## `torc workflows run`
-
-Run a workflow locally on the current node
-
-**Usage:** `torc workflows run [OPTIONS] [WORKFLOW_ID]`
-
-###### **Arguments:**
-
-- `<WORKFLOW_ID>` — ID of the workflow to run (optional - will prompt if not provided)
-
-###### **Options:**
-
-- `-p`, `--poll-interval <POLL_INTERVAL>` — Poll interval in seconds for checking job completion.
-  Default: `5.0`
-- `--max-parallel-jobs <MAX_PARALLEL_JOBS>` — Maximum number of parallel jobs to run (defaults to
-  available CPUs)
-- `--output-dir <OUTPUT_DIR>` — Output directory for job logs and results. Default: `output`
-
 ## `torc init`
 
 Initialize a workflow, including all job statuses

docs/src/core/tutorials/advanced-params.md

@@ -165,7 +165,7 @@ ALL 18 metrics files."
 WORKFLOW_ID=$(torc create grid_search.yaml -f json | jq -r '.id')
 echo "Created workflow: $WORKFLOW_ID"
 
-torc init-jobs $WORKFLOW_ID
+torc init $WORKFLOW_ID
 ```
 
 ## Step 3: Verify the Expansion

docs/src/core/tutorials/diamond.md

@@ -165,7 +165,7 @@ echo "Created workflow: $WORKFLOW_ID"
 touch /tmp/input.txt
 
 # Initialize the workflow (builds dependency graph)
-torc init-jobs $WORKFLOW_ID
+torc init $WORKFLOW_ID
 ```
 
 The `initialize-jobs` command is where Torc:

docs/src/core/tutorials/multi-stage-barrier.md

@@ -259,7 +259,7 @@ Compare this to **10,000 dependencies** without barriers!
 ### Step 4: Run the Workflow
 
 ```bash
-torc workflows run 1
+torc run 1
 ```
 
 ### Step 5: Monitor Progress

docs/src/core/tutorials/simple-params.md

@@ -152,7 +152,7 @@ all 5 process jobs.
 WORKFLOW_ID=$(torc create learning_rate_sweep.yaml -f json | jq -r '.id')
 echo "Created workflow: $WORKFLOW_ID"
 
-torc init-jobs $WORKFLOW_ID
+torc init $WORKFLOW_ID
 ```
 
 ## Step 3: Verify the Expansion

docs/src/core/tutorials/user-data.md

@@ -116,7 +116,7 @@ WORKFLOW_ID=$(torc create user_data_workflow.yaml -f json | jq -r '.id')
 echo "Created workflow: $WORKFLOW_ID"
 
 # Initialize jobs
-torc init-jobs $WORKFLOW_ID
+torc init $WORKFLOW_ID
 ```
 
 ## Step 3: Check Initial State

docs/src/core/workflows/creating-workflows.md

@@ -108,7 +108,7 @@ torc jobs create \
 
 ```bash
 # Initialize the workflow (resolves dependencies)
-torc init-jobs 1
+torc init 1
 
 # Run the workflow
 torc run 1

docs/src/core/workflows/export-import-workflows.md

@@ -167,10 +167,10 @@ file. After import, you need to initialize and run the workflow:
 torc init 456
 
 # Run locally
-torc workflows run 456
+torc run 456
 
 # Or submit to scheduler
-torc workflows submit 456
+torc submit 456
 ```
 
 ### Default Resource Requirements