Add compaction source pruning

AGENTS.md

@@ -1,4 +1,4 @@
-<!-- prpm:snippet:start @agent-workforce/trail-snippet@1.1.0 -->
+<!-- prpm:snippet:start @agent-workforce/trail-snippet@1.1.2 -->
 # Trail
 
 Record your work as a trajectory for future agents and humans to follow.
@@ -82,6 +82,20 @@ When done, complete with a retrospective:
 trail complete --summary "Added JWT auth with refresh tokens" --confidence 0.85
 ```
 
+After completing work, compact the finished trajectory or merged PR into a
+durable summary. When the compacted summary is sufficient, discard the raw
+source trajectories so `.trajectories/index.json` and list output stay focused:
+
+```bash
+trail compact --discard-sources
+# or after a PR merge:
+trail compact --pr 42 --discard-sources
+```
+
+`--discard-sources` removes the source trajectory JSON/Markdown/trace files and
+updates the index. Use it after confirming the compacted artifact is the record
+you want to keep.
+
 **Confidence levels:**
 - 0.9+ : High confidence, well-tested
 - 0.7-0.9 : Good confidence, standard implementation
@@ -122,23 +136,26 @@ trail export <trajectory-id> --format markdown
 
 ## Compacting Trajectories
 
-After a PR merge, compact related trajectories into a single summary:
+After a PR merge, compact related trajectories into a single summary and prune
+raw source trajectories when the summary should replace them:
 
 ```bash
-trail compact --pr 42
+trail compact --pr 42 --discard-sources
 ```
 
 Compact by branch:
 ```bash
-trail compact --branch feature/auth
+trail compact --branch feature/auth --discard-sources
 ```
 
 Compact by commit range:
 ```bash
-trail compact --commits abc123..def456
+trail compact --commits abc123..def456 --discard-sources
 ```
 
-Compaction consolidates decisions and creates a grouped summary, reducing noise while preserving key decisions.
+Compaction consolidates decisions and creates a grouped summary. Adding
+`--discard-sources` makes the compacted artifact the durable record by removing
+the raw trajectories and their index entries.
 
 ## Why Trail?
 
@@ -149,7 +166,7 @@ Your trajectory helps others understand:
 - **What challenges** you faced
 
 Future agents can query past trajectories to learn from your decisions.
-<!-- prpm:snippet:end @agent-workforce/trail-snippet@1.1.0 -->
+<!-- prpm:snippet:end @agent-workforce/trail-snippet@1.1.2 -->
 
 <!-- prpm:snippet:start @agent-relay/agent-relay-snippet@1.1.7 -->
 # Agent Relay

README.md

@@ -132,25 +132,28 @@ trail compact --commits abc1234,def5678  # Trajectories matching specific commit
 trail compact --pr 123                # Trajectories mentioning PR #123
 trail compact --since 7d              # Last 7 days
 trail compact --all                   # Everything (including previously compacted)
+trail compact --pr 123 --discard-sources  # Delete source trajectories and update index after compaction
 ```
 
 ### Automatic Compaction (GitHub Action)
 
-Add these steps to any workflow that runs on PR merge (e.g., your release or publish flow). Requires `ref: ${{ github.event.pull_request.base.ref }}` and `fetch-depth: 0` on checkout, plus `contents: write` permission:
+Add these steps to any workflow that runs on PR merge (e.g., your release or publish flow). Requires `ref: ${{ github.event.pull_request.base.ref }}` and `fetch-depth: 0` on checkout, plus `contents: write` permission.
+
+Use `--discard-sources` when the compacted summary should replace the raw source trajectories. This removes the source JSON/Markdown/trace files and updates `.trajectories/index.json`, reducing future list/search noise.
 
 ```yaml
       - name: Compact trajectories
         run: |
           PR_COMMITS=$(git log ${{ github.event.pull_request.base.sha }}..${{ github.event.pull_request.head.sha }} --format=%H | paste -sd, -)
           OUTPUT=".trajectories/compacted/pr-${{ github.event.pull_request.number }}.json"
           if [ -n "$PR_COMMITS" ]; then
-            npx agent-trajectories compact --commits "$PR_COMMITS" --output "$OUTPUT"
+            npx agent-trajectories compact --commits "$PR_COMMITS" --output "$OUTPUT" --discard-sources
           else
-            npx agent-trajectories compact --pr ${{ github.event.pull_request.number }} --output "$OUTPUT"
+            npx agent-trajectories compact --pr ${{ github.event.pull_request.number }} --output "$OUTPUT" --discard-sources
           fi
       - name: Commit compacted trajectories
         run: |
-          git add .trajectories/compacted/ || true
+          git add .trajectories/ || true
           git diff --cached --quiet || \
             (git commit -m "chore: compact trajectories for PR #${{ github.event.pull_request.number }}" && git push)
 ```

docs/trail-snippet.md

@@ -81,6 +81,20 @@ When done, complete with a retrospective:
 trail complete --summary "Added JWT auth with refresh tokens" --confidence 0.85
 ```
 
+After completing work, compact the finished trajectory or merged PR into a
+durable summary. When the compacted summary is sufficient, discard the raw
+source trajectories so `.trajectories/index.json` and list output stay focused:
+
+```bash
+trail compact --discard-sources
+# or after a PR merge:
+trail compact --pr 42 --discard-sources
+```
+
+`--discard-sources` removes the source trajectory JSON/Markdown/trace files and
+updates the index. Use it after confirming the compacted artifact is the record
+you want to keep.
+
 **Confidence levels:**
 - 0.9+ : High confidence, well-tested
 - 0.7-0.9 : Good confidence, standard implementation
@@ -121,23 +135,26 @@ trail export <trajectory-id> --format markdown
 
 ## Compacting Trajectories
 
-After a PR merge, compact related trajectories into a single summary:
+After a PR merge, compact related trajectories into a single summary and prune
+raw source trajectories when the summary should replace them:
 
 ```bash
-trail compact --pr 42
+trail compact --pr 42 --discard-sources
 ```
 
 Compact by branch (finds trajectories with commits not in the specified base branch):
 ```bash
-trail compact --branch main
+trail compact --branch main --discard-sources
 ```
 
 Compact by specific commits:
 ```bash
-trail compact --commits abc123,def456
+trail compact --commits abc123,def456 --discard-sources
 ```
 
-Compaction consolidates decisions and creates a grouped summary, reducing noise while preserving key decisions.
+Compaction consolidates decisions and creates a grouped summary. Adding
+`--discard-sources` makes the compacted artifact the durable record by removing
+the raw trajectories and their index entries.
 
 ## Why Trail?
 

package.json

@@ -48,9 +48,7 @@
     "type": "git",
     "url": "https://github.com/AgentWorkforce/trajectories"
   },
-  "files": [
-    "dist"
-  ],
+  "files": ["dist"],
   "engines": {
     "node": ">=20.0.0"
   },

prpm.json

@@ -9,7 +9,7 @@
   "packages": [
     {
       "name": "trail-snippet",
-      "version": "1.1.1",
+      "version": "1.1.2",
       "description": "AGENTS.md / CLAUDE.md snippet for agents on how to use trail to record their work",
       "format": "generic",
       "subtype": "snippet",

src/cli/commands/compact.ts

@@ -9,7 +9,13 @@
  */
 
 import { execFileSync } from "node:child_process";
-import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import {
+  existsSync,
+  mkdirSync,
+  readFileSync,
+  unlinkSync,
+  writeFileSync,
+} from "node:fs";
 import { dirname, join } from "node:path";
 import type { Command } from "commander";
 import { getCompactionConfig } from "../../compact/config.js";
@@ -75,6 +81,12 @@ interface IndexEntry {
   compactedInto?: string;
 }
 
+interface TrajectoryIndex {
+  version: number;
+  lastUpdated: string;
+  trajectories: Record<string, IndexEntry>;
+}
+
 interface CompactCommandOptions {
   since?: string;
   until?: string;
@@ -88,10 +100,18 @@ interface CompactCommandOptions {
   mechanical?: boolean;
   focus?: string;
   markdown?: boolean;
+  discardSources?: boolean;
   dryRun?: boolean;
   output?: string;
 }
 
+interface DiscardSourcesSummary {
+  removedIndexEntries: number;
+  deletedJsonFiles: number;
+  deletedMarkdownFiles: number;
+  deletedTraceFiles: number;
+}
+
 interface LLMCompactionPlan {
   messages: Message[];
   estimatedInputTokens: number;
@@ -137,6 +157,10 @@ export function registerCompactCommand(program: Command): void {
     )
     .option("--markdown", "Also write a Markdown companion file")
     .option("--no-markdown", "Skip writing a Markdown companion file")
+    .option(
+      "--discard-sources",
+      "After saving the compaction, delete source trajectory JSON/MD/trace files and remove their index entries",
+    )
     .option("--dry-run", "Preview what would be compacted without saving")
     .option("--output <path>", "Output path for compacted trajectory")
     .action(async (options: CompactCommandOptions) => {
@@ -193,7 +217,15 @@ export function registerCompactCommand(program: Command): void {
           outputPath,
           markdownEnabled,
         );
-        await markTrajectoriesAsCompacted(trajectories, mechanicalCompacted.id);
+        if (options.discardSources) {
+          const discardSummary = discardSourceTrajectories(trajectories);
+          printDiscardSummary(discardSummary);
+        } else {
+          await markTrajectoriesAsCompacted(
+            trajectories,
+            mechanicalCompacted.id,
+          );
+        }
 
         console.log(`\nCompacted trajectory saved to: ${outputPath}`);
         if (markdownEnabled) {
@@ -252,7 +284,12 @@ export function registerCompactCommand(program: Command): void {
       const outputPath =
         options.output || getDefaultOutputPath(compacted, options.workflow);
       saveCompactionArtifacts(compacted, outputPath, markdownEnabled);
-      await markTrajectoriesAsCompacted(trajectories, compacted.id);
+      if (options.discardSources) {
+        const discardSummary = discardSourceTrajectories(trajectories);
+        printDiscardSummary(discardSummary);
+      } else {
+        await markTrajectoriesAsCompacted(trajectories, compacted.id);
+      }
 
       console.log(`\nCompacted trajectory saved to: ${outputPath}`);
       if (markdownEnabled) {
@@ -441,9 +478,7 @@ function getCompactedTrajectoryIds(): Set<string> {
 
     try {
       const indexContent = readFileSync(indexPath, "utf-8");
-      const index = JSON.parse(indexContent) as {
-        trajectories: Record<string, IndexEntry>;
-      };
+      const index = JSON.parse(indexContent) as TrajectoryIndex;
 
       for (const [id, entry] of Object.entries(index.trajectories || {})) {
         if (entry.compactedInto) {
@@ -473,11 +508,7 @@ async function markTrajectoriesAsCompacted(
 
     try {
       const indexContent = readFileSync(indexPath, "utf-8");
-      const index = JSON.parse(indexContent) as {
-        version: number;
-        lastUpdated: string;
-        trajectories: Record<string, IndexEntry>;
-      };
+      const index = JSON.parse(indexContent) as TrajectoryIndex;
 
       let updated = false;
       for (const traj of trajectories) {
@@ -497,6 +528,103 @@ async function markTrajectoriesAsCompacted(
   }
 }
 
+/**
+ * Remove raw source trajectories after a durable compacted artifact has
+ * been written. This keeps compaction as the long-lived record and makes
+ * the index reflect only material that should remain visible.
+ */
+function discardSourceTrajectories(
+  trajectories: Trajectory[],
+): DiscardSourcesSummary {
+  const sourceIds = new Set(trajectories.map((trajectory) => trajectory.id));
+  const summary: DiscardSourcesSummary = {
+    removedIndexEntries: 0,
+    deletedJsonFiles: 0,
+    deletedMarkdownFiles: 0,
+    deletedTraceFiles: 0,
+  };
+
+  for (const searchPath of getSearchPaths()) {
+    const indexPath = join(searchPath, "index.json");
+    if (!existsSync(indexPath)) continue;
+
+    let index: TrajectoryIndex;
+    try {
+      const indexContent = readFileSync(indexPath, "utf-8");
+      const parsedIndex = JSON.parse(indexContent) as unknown;
+      if (!isTrajectoryIndex(parsedIndex)) {
+        continue;
+      }
+      index = parsedIndex;
+    } catch {
+      // Keep behavior consistent with markTrajectoriesAsCompacted: malformed
+      // indexes are ignored instead of blocking an already-saved compaction.
+      continue;
+    }
+
+    let updated = false;
+    for (const id of sourceIds) {
+      const entry = index.trajectories[id];
+      if (!entry) continue;
+
+      if (deleteFileIfExists(entry.path)) {
+        summary.deletedJsonFiles += 1;
+      }
+      if (deleteFileIfExists(getMarkdownOutputPath(entry.path))) {
+        summary.deletedMarkdownFiles += 1;
+      }
+      if (deleteFileIfExists(getTraceOutputPath(entry.path))) {
+        summary.deletedTraceFiles += 1;
+      }
+
+      delete index.trajectories[id];
+      summary.removedIndexEntries += 1;
+      updated = true;
+    }
+
+    if (updated) {
+      index.lastUpdated = new Date().toISOString();
+      writeFileSync(indexPath, JSON.stringify(index, null, 2));
+    }
+  }
+
+  return summary;
+}
+
+function deleteFileIfExists(path: string): boolean {
+  if (!existsSync(path)) {
+    return false;
+  }
+
+  unlinkSync(path);
+  return true;
+}
+
+function isTrajectoryIndex(value: unknown): value is TrajectoryIndex {
+  if (value === null || typeof value !== "object") {
+    return false;
+  }
+
+  const candidate = value as Partial<TrajectoryIndex>;
+  return (
+    candidate.trajectories !== null &&
+    typeof candidate.trajectories === "object" &&
+    !Array.isArray(candidate.trajectories)
+  );
+}
+
+function getTraceOutputPath(outputPath: string): string {
+  return outputPath.endsWith(".json")
+    ? outputPath.slice(0, -".json".length).concat(".trace.json")
+    : `${outputPath}.trace.json`;
+}
+
+function printDiscardSummary(summary: DiscardSourcesSummary): void {
+  console.log(
+    `Discarded source trajectories: ${summary.removedIndexEntries} index entries, ${summary.deletedJsonFiles} JSON files, ${summary.deletedMarkdownFiles} Markdown files, ${summary.deletedTraceFiles} trace files`,
+  );
+}
+
 function parseRelativeDate(input: string): Date {
   // Handle relative dates like "7d", "2w", "1m"
   const match = input.match(/^(\d+)([dwmh])$/);