sysprom 1.13.2 → 1.15.0

package/README.md

@@ -17,44 +17,98 @@ npm install -g github:ExaDev/SysProM
 npx sysprom --help
 ```
 
-Both `sysprom` and `spm` are available as commands.
+Both `sysprom` and `spm` are available as commands — use `sysprom` for new projects.
 
 ## CLI
 
 ```sh
 # Convert between formats
-spm json2md --input .spm.json --output ./.spm
-spm md2json --input ./.spm --output output.spm.json
+sysprom json2md --input .SysProM.json --output ./.SysProM
+sysprom md2json --input ./.SysProM --output output.SysProM.json
 
-# Validate and summarise (auto-detects .spm.json in current directory)
-spm validate
-spm stats
+# Validate and summarise (auto-detects .SysProM.json in current directory)
+sysprom validate
+sysprom stats
 
 # Query nodes and relationships
-spm query nodes --type decision
-spm query node D1
-spm query rels --from D1
-spm query trace I1
-spm query timeline
-spm query state-at 2026-03-22
+sysprom query nodes --type decision
+sysprom query node D1
+sysprom query rels --from D1
+sysprom query trace I1
+sysprom query timeline
+sysprom query state-at 2026-03-22
 
 # Add nodes (ID auto-generated from type prefix if --id omitted)
-spm add invariant --name "New Rule" --description "Must hold"
-spm add decision --name "Choose X" \
+sysprom add invariant --name "New Rule" --description "Must hold"
+sysprom add decision --name "Choose X" \
   --option "OPT-A:Use framework X" --option "OPT-B:Use framework Y" \
   --selected OPT-A --rationale "Lower migration effort"
 
 # Remove nodes
-spm remove INV23
+sysprom remove INV23
 
 # Update nodes, relationships, and metadata
-spm update node D1 --status deprecated
-spm update add-rel D1 affects EL5
-spm update remove-rel D1 affects EL5
-spm update meta --fields version=2
+sysprom update node D1 --status deprecated
+sysprom update add-rel D1 affects EL5
+sysprom update remove-rel D1 affects EL5
+sysprom update meta --fields version=2
+
+# Inference operations (deterministic graph analysis)
+sysprom infer completeness              # Score node completeness (0-1)
+sysprom infer lifecycle                 # Infer lifecycle phases
+sysprom infer impact I1                 # Trace impact from node
+sysprom infer derived                   # Compute transitive closure
+sysprom infer all                       # Run all analyses
 ```
 
-All commands auto-detect the document — they search the current directory for `.spm.json`, `.spm.md`, or `.spm/` (in that priority order), then fall back to `*.spm.json`, `*.spm.md`, or `*.spm/`. Use `--path` to specify an explicit path.
+All commands auto-detect the document — they search the current directory for `.SysProM.json`, `.SysProM.md`, or `.SysProM/` (in that priority order), then fall back to `.spm.json`, `.spm.md`, or `.spm/`. Use `--path` to specify an explicit path. Note: `spm` is an alias for `sysprom` for backwards compatibility.
+
+## MCP Server
+
+SysProM includes an MCP (Model Context Protocol) server exposing 15 tools over stdio transport. Any MCP-compatible agent — Cursor, Windsurf, VS Code Copilot, Cline, or custom clients — can use it.
+
+### Configuration
+
+Add the following to your MCP client's configuration (e.g. `.cursor/mcp.json`, `.vscode/mcp.json`, `cline_mcp_settings.json`, or equivalent):
+
+```json
+{
+  "mcpServers": {
+    "sysprom": {
+      "command": "npx",
+      "args": ["-y", "sysprom", "mcp"]
+    }
+  }
+}
+```
+
+Or via the CLI subcommand (equivalent):
+
+```sh
+sysprom mcp   # starts the MCP server on stdio
+```
+
+### Available Tools
+
+| Tool | Description |
+|------|-------------|
+| `validate` | Validate a SysProM document and return issues |
+| `stats` | Return document statistics |
+| `query-nodes` | Query nodes by type, status, or text |
+| `query-node` | Retrieve a single node by ID |
+| `query-relationships` | Query relationships by source, target, or type |
+| `trace` | Trace refinement chains from a node |
+| `add-node` | Add a new node to the document |
+| `remove-node` | Remove a node by ID |
+| `update-node` | Update fields on an existing node |
+| `add-relationship` | Add a relationship between nodes |
+| `remove-relationship` | Remove a relationship |
+| `infer-completeness` | Score node completeness (0-1) based on refinement relationships |
+| `infer-lifecycle` | Infer lifecycle phase from status and lifecycle fields |
+| `infer-impact` | Trace impact propagation from a starting node |
+| `infer-derived` | Compute transitive closure and inverse relationships |
+
+All tools accept a `path` parameter to specify the SysProM document location.
 
 ## Programmatic API
 
@@ -91,6 +145,12 @@ import {
   removeRelationship,
   updateMetadata,
 
+  // Inference
+  inferCompletenessOp,
+  inferLifecycleOp,
+  inferImpactOp,
+  inferDerivedOp,
+
   // File I/O
   loadDocument,
   saveDocument,
@@ -101,7 +161,7 @@ import {
 } from "sysprom";
 
 // Validate
-const doc = JSON.parse(fs.readFileSync(".spm.json", "utf8"));
+const doc = JSON.parse(fs.readFileSync(".SysProM.json", "utf8"));
 const result = validate(doc);
 console.log(result.valid, result.issues);
 
@@ -169,7 +229,7 @@ SysProM models systems as directed graphs across abstraction layers — intent,
 <tr><td><a href="https://github.com/Priivacy-ai/spec-kitty">Spec Kitty</a></td><td>✅</td><td>🔶</td><td>✅</td><td>🔶</td><td></td><td>🔶</td><td>🔶</td><td>🔶</td><td></td><td></td><td>🔶</td><td>✅</td><td>✅</td><td>✅</td></tr>
 <tr><td><a href="https://github.com/shotgun-sh/shotgun">Shotgun</a></td><td>✅</td><td>🔶</td><td>🔶</td><td></td><td></td><td>🔶</td><td></td><td>🔶</td><td></td><td></td><td>🔶</td><td>🔶</td><td>✅</td><td>🔶</td></tr>
 <tr><td><a href="https://github.com/obra/superpowers">Superpowers</a></td><td>✅</td><td>🔶</td><td>🔶</td><td>🔶</td><td></td><td>🔶</td><td>✅</td><td>🔶</td><td></td><td>✅</td><td>🔶</td><td>✅</td><td>✅</td><td>✅</td></tr>
-<tr><td><strong>SysProM</strong></td><td>✅</td><td>✅</td><td>✅</td><td>✅</td><td>🔶</td><td>✅</td><td>✅</td><td>✅</td><td>✅</td><td></td><td>🔶</td><td>✅</td><td>✅</td><td>✅</td></tr>
+<tr><td><strong>SysProM</strong></td><td>✅</td><td>✅</td><td>✅</td><td>✅</td><td>🔶</td><td>✅</td><td>✅</td><td>✅</td><td>✅</td><td>✅</td><td>🔶</td><td>✅</td><td>✅</td><td>✅</td></tr>
 </tbody>
 </table>
 
@@ -194,7 +254,7 @@ SysProM models systems as directed graphs across abstraction layers — intent,
 SysProM is format-agnostic. This repository includes:
 
 - **JSON** — validated against `schema.json`, supports recursive subsystems
-- **Markdown** — single file (`.spm.md`), multi-document folder, or recursive nested folders with automatic grouping by type
+- **Markdown** — single file (`.SysProM.md`), multi-document folder, or recursive nested folders with automatic grouping by type
 
 Round-trip conversion between JSON and Markdown is supported with zero information loss.
 
@@ -214,29 +274,29 @@ pnpm spm <command>    # Run the CLI from source (e.g. pnpm spm validate ...)
 
 ## Self-Description
 
-`.spm.json` is SysProM describing itself — the specification, its decisions, invariants, changes, and worked examples are all encoded as a SysProM document. The `./.spm/` folder contains the same content as human-readable Markdown.
+`.SysProM.json` is SysProM describing itself — the specification, its decisions, invariants, changes, and worked examples are all encoded as a SysProM document. The `./.SysProM/` folder contains the same content as human-readable Markdown.
 
-All significant activity — decisions, changes, new capabilities, and invariants — should be recorded in the self-describing document. Updates can be made either by editing the Markdown files in `./.spm/` directly or by using the CLI:
+All significant activity — decisions, changes, new capabilities, and invariants — should be recorded in the self-describing document. Updates can be made either by editing the Markdown files in `./.SysProM/` directly or by using the CLI:
 
 ```sh
 # Add a decision via the CLI
-spm add decision --id D23 --name "My Decision" --context "Why this was needed"
+sysprom add decision --id D23 --name "My Decision" --context "Why this was needed"
 
-# Or edit ./.spm/DECISIONS.md directly, then sync
-spm md2json --input ./.spm --output .spm.json
+# Or edit ./.SysProM/DECISIONS.md directly, then sync
+sysprom md2json --input ./.SysProM --output .SysProM.json
 ```
 
 Keep both representations in sync after any change:
 
 ```sh
 # JSON → Markdown
-spm json2md --input .spm.json --output ./.spm
+sysprom json2md --input .SysProM.json --output ./.SysProM
 
 # Markdown → JSON
-spm md2json --input ./.spm --output .spm.json
+sysprom md2json --input ./.SysProM --output .SysProM.json
 ```
 
-> **Important:** Always keep `.spm.json` and `./.spm/` up to date with current activity and in sync with each other. Record all decisions, changes, and new capabilities as they happen. After any change to either representation, run the appropriate conversion command above. Validate with `spm validate` before committing.
+> **Important:** Always keep `.SysProM.json` and `./.SysProM/` up to date with current activity and in sync with each other. Record all decisions, changes, and new capabilities as they happen. After any change to either representation, run the appropriate conversion command above. Validate with `sysprom validate` before committing.
 
 ## Claude Code Plugin
 

package/dist/src/cli/commands/infer.d.ts

@@ -0,0 +1,2 @@
+import type { CommandDef } from "../define-command.js";
+export declare const inferCommand: CommandDef;

package/dist/src/cli/commands/infer.js

@@ -0,0 +1,206 @@
+import pc from "picocolors";
+import * as z from "zod";
+import { readOpts, loadDoc } from "../shared.js";
+import { inferCompletenessOp, inferLifecycleOp, inferImpactOp, inferDerivedOp, } from "../../operations/index.js";
+// ---------------------------------------------------------------------------
+// Presentation helpers
+// ---------------------------------------------------------------------------
+function printCompletenessNode(r) {
+    const scoreColour = r.score === 1 ? pc.green : r.score >= 0.5 ? pc.yellow : pc.red;
+    console.log(`${pc.cyan(r.id.padEnd(12))} ${pc.dim(r.type.padEnd(16))} ${pc.bold(r.name)} ${scoreColour(`[${(r.score * 100).toFixed(0)}%]`)}`);
+    for (const issue of r.issues) {
+        console.log(`  ${pc.dim("•")} ${pc.red(issue)}`);
+    }
+}
+function printLifecycleNode(r) {
+    const phaseColours = {
+        early: pc.blue,
+        middle: pc.yellow,
+        late: pc.green,
+        terminal: pc.red,
+        unknown: pc.dim,
+    };
+    const colour = phaseColours[r.inferredPhase] ?? pc.dim;
+    console.log(`${pc.cyan(r.id.padEnd(12))} ${pc.dim(r.type.padEnd(16))} ${pc.bold(r.name)} ${colour(`[${r.inferredPhase}]`)} ${pc.dim(r.inferredState)}`);
+}
+function printImpactNode(r) {
+    const typeColours = {
+        direct: pc.red,
+        transitive: pc.yellow,
+        potential: pc.blue,
+    };
+    const colour = typeColours[r.impactType] ?? pc.dim;
+    const nodeName = r.node ? r.node.name : "(unknown)";
+    const indent = "  ".repeat(r.distance);
+    console.log(`${indent}${pc.cyan(r.id)} ${pc.dim(`(${String(r.distance)})`)} ${colour(`[${r.impactType}]`)} ${pc.bold(nodeName)}`);
+}
+function printDerivedRelationship(r) {
+    const typeColours = {
+        transitive: pc.yellow,
+        composite: pc.blue,
+        inverse: pc.green,
+    };
+    const colour = typeColours[r.derivationType] ?? pc.dim;
+    console.log(`${pc.cyan(r.from.padEnd(12))} ${colour(r.type.padEnd(20))} ${pc.cyan(r.to)} ${pc.dim(`[${r.derivationType}]`)}`);
+}
+// ---------------------------------------------------------------------------
+// Arg/opt schemas
+// ---------------------------------------------------------------------------
+const impactArgs = z.object({
+    id: z.string().describe("node ID to start impact analysis from"),
+});
+// ---------------------------------------------------------------------------
+// Subcommands
+// ---------------------------------------------------------------------------
+const completenessSubcommand = {
+    name: "completeness",
+    description: inferCompletenessOp.def.description,
+    apiLink: inferCompletenessOp.def.name,
+    opts: readOpts,
+    action(_rawArgs, rawOpts) {
+        const opts = readOpts.parse(rawOpts);
+        const { doc } = loadDoc(opts.path);
+        const result = inferCompletenessOp({ doc });
+        if (opts.json) {
+            console.log(JSON.stringify(result, null, 2));
+        }
+        else {
+            console.log(pc.bold("\nCompleteness Analysis\n") +
+                pc.dim(`Average score: ${(result.averageScore * 100).toFixed(1)}% | `) +
+                pc.green(`${String(result.completeNodes)} complete`) +
+                pc.dim(" | ") +
+                pc.red(`${String(result.incompleteNodes)} incomplete`) +
+                "\n");
+            // Show incomplete nodes first
+            const incomplete = result.nodes.filter((n) => n.score < 1);
+            const complete = result.nodes.filter((n) => n.score === 1);
+            if (incomplete.length > 0) {
+                console.log(pc.dim("Incomplete nodes:"));
+                for (const n of incomplete)
+                    printCompletenessNode(n);
+                console.log();
+            }
+            console.log(pc.dim(`${String(complete.length)} fully complete nodes`));
+        }
+    },
+};
+const lifecycleSubcommand = {
+    name: "lifecycle",
+    description: inferLifecycleOp.def.description,
+    apiLink: inferLifecycleOp.def.name,
+    opts: readOpts,
+    action(_rawArgs, rawOpts) {
+        const opts = readOpts.parse(rawOpts);
+        const { doc } = loadDoc(opts.path);
+        const result = inferLifecycleOp({ doc });
+        if (opts.json) {
+            console.log(JSON.stringify(result, null, 2));
+        }
+        else {
+            console.log(pc.bold("\nLifecycle Analysis\n") +
+                pc.dim(`Early: ${String(result.summary.early)} | Middle: ${String(result.summary.middle)} | Late: ${String(result.summary.late)} | Terminal: ${String(result.summary.terminal)} | Unknown: ${String(result.summary.unknown)}`) +
+                "\n");
+            for (const n of result.nodes)
+                printLifecycleNode(n);
+        }
+    },
+};
+const impactSubcommand = {
+    name: "impact",
+    description: inferImpactOp.def.description,
+    apiLink: inferImpactOp.def.name,
+    args: impactArgs,
+    opts: readOpts,
+    action(rawArgs, rawOpts) {
+        const args = impactArgs.parse(rawArgs);
+        const opts = readOpts.parse(rawOpts);
+        const { doc } = loadDoc(opts.path);
+        const result = inferImpactOp({ doc, startId: args.id });
+        if (opts.json) {
+            console.log(JSON.stringify(result, null, 2));
+        }
+        else {
+            console.log(pc.bold(`\nImpact Analysis from ${args.id}\n`) +
+                pc.dim(`Direct: ${String(result.summary.direct)} | Transitive: ${String(result.summary.transitive)} | Potential: ${String(result.summary.potential)} | Total: ${String(result.summary.total)}`) +
+                "\n");
+            if (result.impactedNodes.length === 0) {
+                console.log(pc.dim("No impacted nodes found"));
+            }
+            else {
+                for (const n of result.impactedNodes)
+                    printImpactNode(n);
+            }
+        }
+    },
+};
+const derivedSubcommand = {
+    name: "derived",
+    description: inferDerivedOp.def.description,
+    apiLink: inferDerivedOp.def.name,
+    opts: readOpts,
+    action(_rawArgs, rawOpts) {
+        const opts = readOpts.parse(rawOpts);
+        const { doc } = loadDoc(opts.path);
+        const result = inferDerivedOp({ doc });
+        if (opts.json) {
+            console.log(JSON.stringify(result, null, 2));
+        }
+        else {
+            console.log(pc.bold("\nDerived Relationships\n") +
+                pc.dim(`Transitive: ${String(result.summary.transitive)} | Composite: ${String(result.summary.composite)} | Inverse: ${String(result.summary.inverse)} | Total: ${String(result.summary.total)}`) +
+                "\n");
+            if (result.derivedRelationships.length === 0) {
+                console.log(pc.dim("No derived relationships found"));
+            }
+            else {
+                for (const r of result.derivedRelationships)
+                    printDerivedRelationship(r);
+            }
+        }
+    },
+};
+const allSubcommand = {
+    name: "all",
+    description: "Run all inference analyses",
+    opts: readOpts,
+    action(_rawArgs, rawOpts) {
+        const opts = readOpts.parse(rawOpts);
+        const { doc } = loadDoc(opts.path);
+        // Completeness
+        console.log(pc.bold("\n=== Completeness ===\n"));
+        const completeness = inferCompletenessOp({ doc });
+        console.log(pc.dim(`Average score: ${(completeness.averageScore * 100).toFixed(1)}% | `) +
+            pc.green(`${String(completeness.completeNodes)} complete`) +
+            pc.dim(" | ") +
+            pc.red(`${String(completeness.incompleteNodes)} incomplete`));
+        // Lifecycle
+        console.log(pc.bold("\n=== Lifecycle ===\n"));
+        const lifecycle = inferLifecycleOp({ doc });
+        console.log(pc.dim(`Early: ${String(lifecycle.summary.early)} | Middle: ${String(lifecycle.summary.middle)} | Late: ${String(lifecycle.summary.late)} | Terminal: ${String(lifecycle.summary.terminal)} | Unknown: ${String(lifecycle.summary.unknown)}`));
+        // Derived
+        console.log(pc.bold("\n=== Derived Relationships ===\n"));
+        const derived = inferDerivedOp({ doc });
+        console.log(pc.dim(`Transitive: ${String(derived.summary.transitive)} | Composite: ${String(derived.summary.composite)} | Inverse: ${String(derived.summary.inverse)} | Total: ${String(derived.summary.total)}`));
+        if (opts.json) {
+            console.log(JSON.stringify({
+                completeness,
+                lifecycle,
+                derived,
+            }, null, 2));
+        }
+    },
+};
+// ---------------------------------------------------------------------------
+// Main command
+// ---------------------------------------------------------------------------
+export const inferCommand = {
+    name: "infer",
+    description: "Infer completeness, lifecycle, impact, and derived relationships",
+    subcommands: [
+        completenessSubcommand,
+        lifecycleSubcommand,
+        impactSubcommand,
+        derivedSubcommand,
+        allSubcommand,
+    ],
+};

package/dist/src/cli/commands/init.js

@@ -15,9 +15,9 @@ function formatToIoFormat(fmt) {
     }
 }
 const suffixMap = {
-    json: ".spm.json",
-    md: ".spm.md",
-    dir: ".spm",
+    json: ".SysProM.json",
+    md: ".SysProM.md",
+    dir: ".SysProM",
 };
 function resolveInitTarget(pathArg, format) {
     const resolved = resolve(pathArg);
@@ -30,8 +30,16 @@ function resolveInitTarget(pathArg, format) {
         };
     }
     const fmt = format ?? "dir";
+    const suffix = suffixMap[fmt];
+    // If path already ends with the correct suffix, use it as-is
+    if (resolved.endsWith(suffix)) {
+        return {
+            outputPath: resolved,
+            ioFormat: formatToIoFormat(fmt),
+        };
+    }
     return {
-        outputPath: `${resolved}${suffixMap[fmt]}`,
+        outputPath: `${resolved}${suffix}`,
         ioFormat: formatToIoFormat(fmt),
     };
 }

package/dist/src/cli/program.js

@@ -43,6 +43,7 @@ import { speckitCommand } from "./commands/speckit.js";
 import { taskCommand } from "./commands/task.js";
 import { planCommand } from "./commands/plan.js";
 import { syncCommandDef } from "./commands/sync.js";
+import { inferCommand } from "./commands/infer.js";
 export const program = new Command();
 program
     .name("sysprom")
@@ -71,6 +72,7 @@ export const commands = [
     taskCommand,
     planCommand,
     syncCommandDef,
+    inferCommand,
 ];
 for (const cmd of commands) {
     buildCommander(cmd, program);

package/dist/src/cli/shared.d.ts

@@ -6,19 +6,24 @@ export declare const noArgs: z.ZodObject<{}, z.core.$strict>;
 /**
  * Resolve a SysProM document path. If no explicit path is given, search the
  * working directory by priority:
- *   1. .spm.json     2. .spm.md     3. .spm/
- *   4. .sysprom.json  5. .sysprom.md  6. .sysprom/
- *   7. *.spm.json    8. *.spm.md    9. *.spm/
- *  10. *.sysprom.json 11. *.sysprom.md 12. *.sysprom/
+ *   1. .SysProM.json   2. .SysProM.md   3. .SysProM/
+ *   4. .spm.json       5. .spm.md       6. .spm/
+ *   7. .sysprom.json   8. .sysprom.md   9. .sysprom/
+ *  10. *.SysProM.json  11. *.SysProM.md 12. *.SysProM/
+ *  13. *.spm.json     14. *.spm.md     15. *.spm/
+ *  16. *.sysprom.json 17. *.sysprom.md 18. *.sysprom/
  *
- * All matching is case-insensitive. Glob tiers must have exactly one match.
+ * Matching is case-insensitive for base names and directory matches.
+ * Files like .SysProM.json, .sysprom.json, and .SYSPROM.JSON are treated
+ * as equivalent and all match the .SysProM.json priority tier.
+ * Glob tiers must have exactly one match.
  * @param input - Explicit document path, or undefined for auto-detection.
  * @param cwd - Working directory to search from (defaults to `.`).
  * @returns The resolved document path.
  * @example
  * ```ts
- * resolveInput() // => auto-detects ".spm.json" in cwd
- * resolveInput("my-doc.spm.json") // => "my-doc.spm.json"
+ * resolveInput() // => auto-detects ".SysProM.json" in cwd
+ * resolveInput("my-doc.SysProM.json") // => "my-doc.SysProM.json"
  * ```
  */
 export declare function resolveInput(input?: string, cwd?: string): string;

package/dist/src/cli/shared.js

@@ -19,27 +19,34 @@ const pathOpt = z
 /**
  * Resolve a SysProM document path. If no explicit path is given, search the
  * working directory by priority:
- *   1. .spm.json     2. .spm.md     3. .spm/
- *   4. .sysprom.json  5. .sysprom.md  6. .sysprom/
- *   7. *.spm.json    8. *.spm.md    9. *.spm/
- *  10. *.sysprom.json 11. *.sysprom.md 12. *.sysprom/
+ *   1. .SysProM.json   2. .SysProM.md   3. .SysProM/
+ *   4. .spm.json       5. .spm.md       6. .spm/
+ *   7. .sysprom.json   8. .sysprom.md   9. .sysprom/
+ *  10. *.SysProM.json  11. *.SysProM.md 12. *.SysProM/
+ *  13. *.spm.json     14. *.spm.md     15. *.spm/
+ *  16. *.sysprom.json 17. *.sysprom.md 18. *.sysprom/
  *
- * All matching is case-insensitive. Glob tiers must have exactly one match.
+ * Matching is case-insensitive for base names and directory matches.
+ * Files like .SysProM.json, .sysprom.json, and .SYSPROM.JSON are treated
+ * as equivalent and all match the .SysProM.json priority tier.
+ * Glob tiers must have exactly one match.
  * @param input - Explicit document path, or undefined for auto-detection.
  * @param cwd - Working directory to search from (defaults to `.`).
  * @returns The resolved document path.
  * @example
  * ```ts
- * resolveInput() // => auto-detects ".spm.json" in cwd
- * resolveInput("my-doc.spm.json") // => "my-doc.spm.json"
+ * resolveInput() // => auto-detects ".SysProM.json" in cwd
+ * resolveInput("my-doc.SysProM.json") // => "my-doc.SysProM.json"
  * ```
  */
 export function resolveInput(input, cwd) {
     if (input)
         return input;
     const dir = resolve(cwd ?? ".");
-    // Exact names to check, in priority order (case-insensitive)
     const exactNames = [
+        ".SysProM.json",
+        ".SysProM.md",
+        ".SysProM",
         ".spm.json",
         ".spm.md",
         ".spm",
@@ -48,9 +55,42 @@ export function resolveInput(input, cwd) {
         ".sysprom",
     ];
     const entries = readdirSync(dir);
+    // Phase 1: Try exact case-sensitive matches first
     for (const name of exactNames) {
-        const isDirSuffix = name.endsWith(".spm") || name.endsWith(".sysprom");
-        const found = entries.filter((e) => e.toLowerCase() === name);
+        const isDirSuffix = name.endsWith(".SysProM") ||
+            name.endsWith(".spm") ||
+            name.endsWith(".sysprom");
+        const found = entries.filter((e) => e === name);
+        if (found.length === 1) {
+            // Before returning, check for case-variant collisions on case-sensitive
+            // filesystems (e.g. both .spm.json and .SPM.json exist).
+            const nameLower = name.toLowerCase();
+            const caseVariants = entries.filter((e) => e !== name && e.toLowerCase() === nameLower);
+            if (caseVariants.length > 0) {
+                throw new Error(`Multiple SysProM documents found: ${[name, ...caseVariants].join(", ")}. Specify one explicitly.`);
+            }
+            const candidate = join(dir, found[0]);
+            if (isDirSuffix) {
+                try {
+                    if (statSync(candidate).isDirectory())
+                        return candidate;
+                }
+                catch {
+                    /* skip */
+                }
+            }
+            else {
+                return candidate;
+            }
+        }
+    }
+    // Phase 2: Try case-insensitive matches (supports case variations like .SPM.JSON)
+    for (const name of exactNames) {
+        const isDirSuffix = name.endsWith(".SysProM") ||
+            name.endsWith(".spm") ||
+            name.endsWith(".sysprom");
+        const nameLower = name.toLowerCase();
+        const found = entries.filter((e) => e.toLowerCase() === nameLower);
         if (found.length > 1) {
             throw new Error(`Multiple SysProM documents found: ${found.join(", ")}. Specify one explicitly.`);
         }
@@ -72,6 +112,9 @@ export function resolveInput(input, cwd) {
     }
     // Glob suffixes in priority order (case-insensitive)
     const globSuffixes = [
+        ".SysProM.json",
+        ".SysProM.md",
+        ".SysProM",
         ".spm.json",
         ".spm.md",
         ".spm",
@@ -80,11 +123,16 @@ export function resolveInput(input, cwd) {
         ".sysprom",
     ];
     for (const suffix of globSuffixes) {
-        const isDirSuffix = suffix === ".spm" || suffix === ".sysprom";
+        const isDirSuffix = suffix === ".SysProM" || suffix === ".spm" || suffix === ".sysprom";
+        const suffixLower = suffix.toLowerCase();
         const matches = entries
             .filter((e) => {
             const lower = e.toLowerCase();
-            return lower.endsWith(suffix) && lower !== suffix;
+            // Match files ending with this suffix (case-insensitive) that don't start with "."
+            // and are not exact matches (those were already checked)
+            return (lower.endsWith(suffixLower) &&
+                lower !== suffixLower &&
+                !e.startsWith("."));
         })
             .map((e) => join(dir, e))
             .filter((p) => {

package/dist/src/index.d.ts

@@ -6,7 +6,7 @@
  * @packageDocumentation
  */
 export { SysProMDocument, Node, Relationship, NodeType, NodeStatus, RelationshipType, Text, Option, Operation, Task, ExternalReference, ExternalReferenceRole, Metadata, NODE_TYPE_LABELS, NODE_LABEL_TO_TYPE, RELATIONSHIP_TYPE_LABELS, RELATIONSHIP_LABEL_TO_TYPE, EXTERNAL_REFERENCE_ROLE_LABELS, EXTERNAL_REFERENCE_LABEL_TO_ROLE, NODE_STATUSES, NODE_FILE_MAP, NODE_ID_PREFIX, toJSONSchema, } from "./schema.js";
-export { defineOperation, type OperationDef, type DefinedOperation, addNodeOp, removeNodeOp, updateNodeOp, addRelationshipOp, removeRelationshipOp, updateMetadataOp, nextIdOp, initDocumentOp, addPlanTaskOp, updatePlanTaskOp, markTaskDoneOp, markTaskUndoneOp, taskListOp, planInitOp, planAddTaskOp, planStatusOp, planProgressOp, planGateOp, queryNodesOp, queryNodeOp, queryRelationshipsOp, traceFromNodeOp, timelineOp, nodeHistoryOp, stateAtOp, validateOp, statsOp, searchOp, checkOp, graphOp, renameOp, jsonToMarkdownOp, markdownToJsonOp, speckitImportOp, speckitExportOp, speckitSyncOp, speckitDiffOp, type RemoveResult, type ValidationResult, type DocumentStats, type NodeDetail, type TraceNode, type TimelineEvent, type NodeState, type PlanStatusResult, type PhaseProgressResult, type GateResultOutput, type SyncResult, type DiffResult, } from "./operations/index.js";
+export { defineOperation, type OperationDef, type DefinedOperation, addNodeOp, removeNodeOp, updateNodeOp, addRelationshipOp, removeRelationshipOp, updateMetadataOp, nextIdOp, initDocumentOp, addPlanTaskOp, updatePlanTaskOp, markTaskDoneOp, markTaskUndoneOp, taskListOp, planInitOp, planAddTaskOp, planStatusOp, planProgressOp, planGateOp, queryNodesOp, queryNodeOp, queryRelationshipsOp, traceFromNodeOp, timelineOp, nodeHistoryOp, stateAtOp, validateOp, statsOp, searchOp, checkOp, graphOp, renameOp, jsonToMarkdownOp, markdownToJsonOp, speckitImportOp, speckitExportOp, speckitSyncOp, speckitDiffOp, inferCompletenessOp, inferLifecycleOp, inferImpactOp, inferDerivedOp, type RemoveResult, type ValidationResult, type DocumentStats, type NodeDetail, type TraceNode, type TimelineEvent, type NodeState, type PlanStatusResult, type PhaseProgressResult, type GateResultOutput, type SyncResult, type DiffResult, type CompletenessOutput, type LifecycleOutput, type ImpactOutput, type DerivedOutput, } from "./operations/index.js";
 export { jsonToMarkdownSingle, jsonToMarkdownMultiDoc, jsonToMarkdown, type ConvertOptions, } from "./json-to-md.js";
 export { markdownSingleToJson, markdownMultiDocToJson, markdownToJson, } from "./md-to-json.js";
 export { RELATIONSHIP_ENDPOINT_TYPES, isValidEndpointPair, } from "./endpoint-types.js";

package/dist/src/index.js

@@ -8,7 +8,7 @@
 // Schema types and validators
 export { SysProMDocument, Node, Relationship, NodeType, NodeStatus, RelationshipType, Text, Option, Operation, Task, ExternalReference, ExternalReferenceRole, Metadata, NODE_TYPE_LABELS, NODE_LABEL_TO_TYPE, RELATIONSHIP_TYPE_LABELS, RELATIONSHIP_LABEL_TO_TYPE, EXTERNAL_REFERENCE_ROLE_LABELS, EXTERNAL_REFERENCE_LABEL_TO_ROLE, NODE_STATUSES, NODE_FILE_MAP, NODE_ID_PREFIX, toJSONSchema, } from "./schema.js";
 // Operations (single source of truth for domain logic + metadata)
-export { defineOperation, addNodeOp, removeNodeOp, updateNodeOp, addRelationshipOp, removeRelationshipOp, updateMetadataOp, nextIdOp, initDocumentOp, addPlanTaskOp, updatePlanTaskOp, markTaskDoneOp, markTaskUndoneOp, taskListOp, planInitOp, planAddTaskOp, planStatusOp, planProgressOp, planGateOp, queryNodesOp, queryNodeOp, queryRelationshipsOp, traceFromNodeOp, timelineOp, nodeHistoryOp, stateAtOp, validateOp, statsOp, searchOp, checkOp, graphOp, renameOp, jsonToMarkdownOp, markdownToJsonOp, speckitImportOp, speckitExportOp, speckitSyncOp, speckitDiffOp, } from "./operations/index.js";
+export { defineOperation, addNodeOp, removeNodeOp, updateNodeOp, addRelationshipOp, removeRelationshipOp, updateMetadataOp, nextIdOp, initDocumentOp, addPlanTaskOp, updatePlanTaskOp, markTaskDoneOp, markTaskUndoneOp, taskListOp, planInitOp, planAddTaskOp, planStatusOp, planProgressOp, planGateOp, queryNodesOp, queryNodeOp, queryRelationshipsOp, traceFromNodeOp, timelineOp, nodeHistoryOp, stateAtOp, validateOp, statsOp, searchOp, checkOp, graphOp, renameOp, jsonToMarkdownOp, markdownToJsonOp, speckitImportOp, speckitExportOp, speckitSyncOp, speckitDiffOp, inferCompletenessOp, inferLifecycleOp, inferImpactOp, inferDerivedOp, } from "./operations/index.js";
 // Conversion
 export { jsonToMarkdownSingle, jsonToMarkdownMultiDoc, jsonToMarkdown, } from "./json-to-md.js";
 export { markdownSingleToJson, markdownMultiDocToJson, markdownToJson, } from "./md-to-json.js";