fix(cli): replace stdin auto-detect with explicit --stdin flag

.claude/skills/swamp-model/SKILL.md

@@ -59,31 +59,31 @@ definitions referenced across multiple workflows.
 
 ## Quick Reference
 
-| Task                | Command                                                          |
-| ------------------- | ---------------------------------------------------------------- |
-| Search model types  | `swamp model type search [query] --json`                         |
-| Describe a type     | `swamp model type describe <type> --json`                        |
-| Create model input  | `swamp model create <type> <name> --json`                        |
-| Create with args    | `swamp model create <type> <name> --global-arg key=value --json` |
-| Search models       | `swamp model search [query] --json`                              |
-| Get model details   | `swamp model get <id_or_name> --json`                            |
-| Edit model input    | `swamp model edit [id_or_name]`                                  |
-| Delete a model      | `swamp model delete <id_or_name> --json`                         |
-| Validate model      | `swamp model validate [id_or_name] --json`                       |
-| Validate by label   | `swamp model validate [id_or_name] --label policy --json`        |
-| Validate by method  | `swamp model validate [id_or_name] --method create --json`       |
-| Evaluate input(s)   | `swamp model evaluate [id_or_name] --json`                       |
-| Run a method        | `swamp model method run <id_or_name> <method>`                   |
-| Run with inputs     | `swamp model method run <name> <method> --input key=value`       |
-| Run from stdin      | `echo '{"k":"v"}' \| swamp model method run <name> <method>`     |
-| Direct type exec    | `swamp model @<type> method run <method> <name> --input k=v`     |
-| Skip all checks     | `swamp model method run <name> <method> --skip-checks`           |
-| Skip check by name  | `swamp model method run <name> <method> --skip-check <n>`        |
-| Skip check by label | `swamp model method run <name> <method> --skip-check-label <l>`  |
-| Search outputs      | `swamp model output search [query] --json`                       |
-| Get output details  | `swamp model output get <output_or_model> --json`                |
-| View output logs    | `swamp model output logs <output_id> --json`                     |
-| View output data    | `swamp model output data <output_id> --json`                     |
+| Task                | Command                                                              |
+| ------------------- | -------------------------------------------------------------------- |
+| Search model types  | `swamp model type search [query] --json`                             |
+| Describe a type     | `swamp model type describe <type> --json`                            |
+| Create model input  | `swamp model create <type> <name> --json`                            |
+| Create with args    | `swamp model create <type> <name> --global-arg key=value --json`     |
+| Search models       | `swamp model search [query] --json`                                  |
+| Get model details   | `swamp model get <id_or_name> --json`                                |
+| Edit model input    | `swamp model edit [id_or_name]`                                      |
+| Delete a model      | `swamp model delete <id_or_name> --json`                             |
+| Validate model      | `swamp model validate [id_or_name] --json`                           |
+| Validate by label   | `swamp model validate [id_or_name] --label policy --json`            |
+| Validate by method  | `swamp model validate [id_or_name] --method create --json`           |
+| Evaluate input(s)   | `swamp model evaluate [id_or_name] --json`                           |
+| Run a method        | `swamp model method run <id_or_name> <method>`                       |
+| Run with inputs     | `swamp model method run <name> <method> --input key=value`           |
+| Run from stdin      | `echo '{"k":"v"}' \| swamp model method run <name> <method> --stdin` |
+| Direct type exec    | `swamp model @<type> method run <method> <name> --input k=v`         |
+| Skip all checks     | `swamp model method run <name> <method> --skip-checks`               |
+| Skip check by name  | `swamp model method run <name> <method> --skip-check <n>`            |
+| Skip check by label | `swamp model method run <name> <method> --skip-check-label <l>`      |
+| Search outputs      | `swamp model output search [query] --json`                           |
+| Get output details  | `swamp model output get <output_or_model> --json`                    |
+| View output logs    | `swamp model output logs <output_id> --json`                         |
+| View output data    | `swamp model output data <output_id> --json`                         |
 
 ## Repository Structure
 
@@ -424,9 +424,9 @@ swamp model method run my-deploy create --input config.timeout=30  # dot notatio
 swamp model method run my-deploy create --input 'tags:json=["prod","west"]'  # :json suffix for arrays/objects
 swamp model method run my-deploy create --input '{"environment": "prod"}'  # legacy single-shot JSON
 swamp model method run my-deploy create --input-file inputs.yaml
-echo '{"environment": "prod"}' | swamp model method run my-deploy create  # stdin auto-detected
-printf '{"environment":"dev"}\n{"environment":"prod"}' | swamp model method run my-deploy create  # NDJSON: one run per line
-swamp data query 'modelName == "source"' --json | jq -c '.results[] | {environment: .attributes.env}' | swamp model method run my-deploy create  # pipe composition
+echo '{"environment": "prod"}' | swamp model method run my-deploy create --stdin
+printf '{"environment":"dev"}\n{"environment":"prod"}' | swamp model method run my-deploy create --stdin  # NDJSON: one run per line
+swamp data query 'modelName == "source"' --json | jq -c '.results[] | {environment: .attributes.env}' | swamp model method run my-deploy create --stdin
 swamp model method run my-deploy create --last-evaluated
 swamp model method run my-deploy create --skip-checks
 swamp model method run my-deploy create --skip-check valid-region

.claude/skills/swamp-model/references/examples.md

@@ -204,19 +204,19 @@ swamp model method run my-deploy deploy --input '{"environment": "production"}'
 # YAML file input
 swamp model method run my-deploy deploy --input-file inputs.yaml
 
-# Piped stdin (auto-detected, no flag needed)
-echo '{"environment": "production"}' | swamp model method run my-deploy deploy
+# Piped stdin (explicit --stdin flag required)
+echo '{"environment": "production"}' | swamp model method run my-deploy deploy --stdin
 
 # NDJSON from stdin: one run per line
-printf '{"environment":"dev"}\n{"environment":"prod"}' | swamp model method run my-deploy deploy
+printf '{"environment":"dev"}\n{"environment":"prod"}' | swamp model method run my-deploy deploy --stdin
 
 # Pipe from data query via jq
 swamp data query 'modelName == "source"' --json \
   | jq -c '.results[] | {environment: .attributes.env}' \
-  | swamp model method run my-deploy deploy
+  | swamp model method run my-deploy deploy --stdin
 
 # Stdin + --input overrides (--input wins on conflict)
-echo '{"environment": "dev"}' | swamp model method run my-deploy deploy --input dryRun=true
+echo '{"environment": "dev"}' | swamp model method run my-deploy deploy --stdin --input dryRun=true
 ```
 
 **Input file format (inputs.yaml)**:

.claude/skills/swamp-model/references/scenarios.md

@@ -217,8 +217,8 @@ swamp model validate my-instance --json
 ```
 User wants runtime parameterization → Use inputs schema
 Values change per invocation → --input or --input-file
-Values come from another command → Pipe stdin (auto-detected)
-Batch run over query results → data query --json | jq | method run
+Values come from another command → Pipe with --stdin
+Batch run over query results → data query --json | jq | method run --stdin
 ```
 
 ### Step-by-Step
@@ -302,14 +302,14 @@ swamp model method run my-deploy deploy --input-file inputs/production.yaml
 **6. Alternative: Pipe inputs from another command**
 
 ```bash
-# Stdin is auto-detected — pipe JSON and it becomes the inputs
+# Pass --stdin to read piped JSON as inputs
 echo '{"environment": "production", "replicas": 5}' \
-  | swamp model method run my-deploy deploy
+  | swamp model method run my-deploy deploy --stdin
 
 # Batch: run deploy for each result from a data query
 swamp data query 'modelName == "infra" && attributes.status == "pending"' --json \
   | jq -c '.results[] | {environment: .attributes.env, replicas: .attributes.count}' \
-  | swamp model method run my-deploy deploy
+  | swamp model method run my-deploy deploy --stdin
 ```
 
 ### CEL Paths Used

.claude/skills/swamp-workflow/SKILL.md

@@ -24,25 +24,25 @@ run.
 
 ## Quick Reference
 
-| Task               | Command                                                |
-| ------------------ | ------------------------------------------------------ |
-| Get schema         | `swamp workflow schema get --json`                     |
-| Search workflows   | `swamp workflow search [query] --json`                 |
-| Get a workflow     | `swamp workflow get <id_or_name> --json`               |
-| Create a workflow  | `swamp workflow create <name> --json`                  |
-| Edit a workflow    | `swamp workflow edit [id_or_name]`                     |
-| Delete a workflow  | `swamp workflow delete <id_or_name> --json`            |
-| Validate workflow  | `swamp workflow validate [id_or_name] --json`          |
-| Evaluate workflow  | `swamp workflow evaluate <id_or_name> --json`          |
-| Run a workflow     | `swamp workflow run <id_or_name>`                      |
-| Run with inputs    | `swamp workflow run <id_or_name> --input key=value`    |
-| Run from stdin     | `echo '{"k":"v"}' \| swamp workflow run <id_or_name>`  |
-| View run history   | `swamp workflow history search --json`                 |
-| Get latest run     | `swamp workflow history get <workflow> --json`         |
-| View run logs      | `swamp workflow history logs <run_or_workflow> --json` |
-| List workflow data | `swamp data list --workflow <name> --json`             |
-| Query wf data      | `swamp data query 'tags.workflow == "<name>"'`         |
-| Get workflow data  | `swamp data get --workflow <name> <data_name> --json`  |
+| Task               | Command                                                       |
+| ------------------ | ------------------------------------------------------------- |
+| Get schema         | `swamp workflow schema get --json`                            |
+| Search workflows   | `swamp workflow search [query] --json`                        |
+| Get a workflow     | `swamp workflow get <id_or_name> --json`                      |
+| Create a workflow  | `swamp workflow create <name> --json`                         |
+| Edit a workflow    | `swamp workflow edit [id_or_name]`                            |
+| Delete a workflow  | `swamp workflow delete <id_or_name> --json`                   |
+| Validate workflow  | `swamp workflow validate [id_or_name] --json`                 |
+| Evaluate workflow  | `swamp workflow evaluate <id_or_name> --json`                 |
+| Run a workflow     | `swamp workflow run <id_or_name>`                             |
+| Run with inputs    | `swamp workflow run <id_or_name> --input key=value`           |
+| Run from stdin     | `echo '{"k":"v"}' \| swamp workflow run <id_or_name> --stdin` |
+| View run history   | `swamp workflow history search --json`                        |
+| Get latest run     | `swamp workflow history get <workflow> --json`                |
+| View run logs      | `swamp workflow history logs <run_or_workflow> --json`        |
+| List workflow data | `swamp data list --workflow <name> --json`                    |
+| Query wf data      | `swamp data query 'tags.workflow == "<name>"'`                |
+| Get workflow data  | `swamp data get --workflow <name> <data_name> --json`         |
 
 ## Repository Structure
 
@@ -259,13 +259,13 @@ swamp workflow run my-workflow --input environment=production --input replicas=3
 swamp workflow run my-workflow --input 'tags:json=["prod","west"]'  # :json suffix for arrays/objects
 swamp workflow run my-workflow --input '{"environment": "production"}'  # legacy single-shot JSON
 swamp workflow run my-workflow --input-file inputs.yaml
-echo '{"environment": "prod"}' | swamp workflow run my-workflow  # stdin auto-detected
-printf '{"environment":"dev"}\n{"environment":"prod"}' | swamp workflow run my-workflow  # NDJSON: one run per line
+echo '{"environment": "prod"}' | swamp workflow run my-workflow --stdin
+printf '{"environment":"dev"}\n{"environment":"prod"}' | swamp workflow run my-workflow --stdin  # NDJSON: one run per line
 swamp workflow run my-workflow --last-evaluated  # Use pre-evaluated workflow
 ```
 
-Piped stdin is auto-detected. JSON objects, JSON arrays, NDJSON (one JSON per
-line), and YAML are supported. Multiple items (array or NDJSON) produce one
+Pass `--stdin` to read piped input. JSON objects, JSON arrays, NDJSON (one JSON
+per line), and YAML are supported. Multiple items (array or NDJSON) produce one
 workflow run per item. `--input` key=value overrides are deep-merged onto each
 stdin item.
 
@@ -274,7 +274,8 @@ stdin item.
 | Flag                | Description                                                        |
 | ------------------- | ------------------------------------------------------------------ |
 | `--input <value>`   | Input values (key=value repeatable, or JSON)                       |
-| `--input-file <f>`  | Input values from YAML file (cannot combine with piped stdin)      |
+| `--input-file <f>`  | Input values from YAML file (cannot combine with `--stdin`)        |
+| `--stdin`           | Read inputs from stdin (piped data)                                |
 | `--last-evaluated`  | Use previously evaluated workflow (skip eval and input validation) |
 | `--driver <driver>` | Override execution driver for all steps (e.g. `raw`, `docker`)     |
 

.claude/skills/swamp-workflow/references/scenarios.md

@@ -580,17 +580,17 @@ Run a workflow for each result from a data query using Unix pipes and `jq`.
 # Run workflow once per pending item from a data query
 swamp data query 'modelName == "source" && attributes.status == "pending"' --json \
   | jq -c '.results[] | {environment: .attributes.env}' \
-  | swamp workflow run deploy-pipeline
+  | swamp workflow run deploy-pipeline --stdin
 
 # NDJSON: run workflow once per line
 printf '{"environment":"dev"}\n{"environment":"prod"}' \
-  | swamp workflow run deploy-pipeline
+  | swamp workflow run deploy-pipeline --stdin
 
 # Stdin + --input overrides (--input wins on conflict)
 echo '{"environment": "dev"}' \
-  | swamp workflow run deploy-pipeline --input dryRun=true
+  | swamp workflow run deploy-pipeline --stdin --input dryRun=true
 ```
 
-Stdin is auto-detected — no flag needed. JSON objects, JSON arrays, NDJSON, and
-YAML are all supported. Multiple items produce one workflow run per item.
-Execution stops on the first failure.
+Pass `--stdin` to read piped input. JSON objects, JSON arrays, NDJSON, and YAML
+are all supported. Multiple items produce one workflow run per item. Execution
+stops on the first failure.

design/inputs.md

@@ -233,10 +233,10 @@ via `--input-file` with YAML/JSON, or via the legacy single-shot
 
 ### Reading inputs from stdin
 
-Both `method run` and `workflow run` auto-detect piped stdin. When data is piped
-to the command, it is read and parsed as inputs — no flag needed. This enables
-Unix pipe composition following the same pattern as `vault put`, `model edit`,
-and `workflow edit`.
+Both `method run` and `workflow run` accept piped stdin via the `--stdin` flag.
+When `--stdin` is passed, the command reads stdin until EOF and parses it as
+inputs. This enables Unix pipe composition following the same pattern as `jq -n`
+(explicit opt-in).
 
 The input format is detected automatically:
 
@@ -250,22 +250,22 @@ executed once per item. Each execution is discrete — it produces its own data
 artifacts, runs pre-flight checks, and reports independently. Execution stops on
 the first failure.
 
-Piped stdin and `--input-file` cannot be combined. `--input` key=value overrides
-can be combined with piped stdin — they are deep-merged onto each stdin item (the
+`--stdin` and `--input-file` cannot be combined. `--input` key=value overrides
+can be combined with `--stdin` — they are deep-merged onto each stdin item (the
 `--input` values win on conflict).
 
 ```sh
 # Single JSON object from stdin
-echo '{"run": "echo hello"}' | swamp model method run my-model execute
+echo '{"run": "echo hello"}' | swamp model method run my-model execute --stdin
 
 # NDJSON: run method once per line
 printf '{"run":"echo a"}\n{"run":"echo b"}' \
-  | swamp model method run my-model execute
+  | swamp model method run my-model execute --stdin
 
 # Pipe from data query via jq, with static overrides
 swamp data query 'modelName == "source"' --json \
   | jq -c '.results[] | {run: .attributes.command}' \
-  | swamp model method run target-model execute --input env=prod
+  | swamp model method run target-model execute --stdin --input env=prod
 ```
 
 ## Input Routing for Direct Type Execution

src/cli/commands/model_method_run.ts

@@ -89,11 +89,11 @@ export const modelMethodRunCommand = new Command()
   )
   .example(
     "Pipe inputs from stdin",
-    'echo \'{"env":"prod"}\' | swamp model method run my-server deploy',
+    'echo \'{"env":"prod"}\' | swamp model method run my-server deploy --stdin',
   )
   .example(
     "Batch run via NDJSON from stdin",
-    'printf \'{"env":"dev"}\\n{"env":"prod"}\' | swamp model method run my-server deploy',
+    'printf \'{"env":"dev"}\\n{"env":"prod"}\' | swamp model method run my-server deploy --stdin',
   )
   .description(
     "Execute a method on a model. With @type prefix, auto-creates the definition if needed.",
@@ -115,8 +115,9 @@ export const modelMethodRunCommand = new Command()
   })
   .option(
     "--input-file <file:string>",
-    "Input values from YAML file (cannot combine with piped stdin)",
+    "Input values from YAML file (cannot combine with --stdin)",
   )
+  .option("--stdin", "Read inputs from stdin (piped data)", { default: false })
   .option(
     "--tag <tag:string>",
     "Add tag to produced data (KEY=VALUE, repeatable)",
@@ -198,8 +199,7 @@ export const modelMethodRunCommand = new Command()
       ctx.logger
         .debug`Running method '${methodName}' on model: ${modelIdOrName}`;
 
-      // Auto-detect piped stdin (returns null when stdin is a TTY)
-      const stdinContent = await readStdin();
+      const stdinContent = options.stdin ? await readStdin() : null;
       let stdinItems: Record<string, unknown>[] | null = null;
       if (stdinContent !== null) {
         if (options.inputFile) {

src/cli/commands/workflow_run.ts

@@ -92,11 +92,11 @@ export const workflowRunCommand = new Command()
   .example("Skip reports", "swamp workflow run deploy-pipeline --skip-reports")
   .example(
     "Pipe inputs from stdin",
-    'echo \'{"env":"prod"}\' | swamp workflow run deploy-pipeline',
+    'echo \'{"env":"prod"}\' | swamp workflow run deploy-pipeline --stdin',
   )
   .example(
     "Batch run via NDJSON from stdin",
-    'printf \'{"env":"dev"}\\n{"env":"prod"}\' | swamp workflow run deploy-pipeline',
+    'printf \'{"env":"dev"}\\n{"env":"prod"}\' | swamp workflow run deploy-pipeline --stdin',
   )
   .arguments("<workflow_id_or_name:workflow_name>")
   .option(
@@ -113,8 +113,9 @@ export const workflowRunCommand = new Command()
   })
   .option(
     "--input-file <file:string>",
-    "Input values from YAML file (cannot combine with piped stdin)",
+    "Input values from YAML file (cannot combine with --stdin)",
   )
+  .option("--stdin", "Read inputs from stdin (piped data)", { default: false })
   .option(
     "--tag <tag:string>",
     "Add tag to produced data (KEY=VALUE, repeatable)",
@@ -174,8 +175,7 @@ export const workflowRunCommand = new Command()
 
     const lastEvaluated = options.lastEvaluated as boolean;
 
-    // Auto-detect piped stdin (returns null when stdin is a TTY)
-    const stdinContent = await readStdin();
+    const stdinContent = options.stdin ? await readStdin() : null;
     let stdinItems: Record<string, unknown>[] | null = null;
     if (stdinContent !== null) {
       if (options.inputFile) {