diff --git a/agents/gsd-user-profiler.md b/agents/gsd-user-profiler.md
index c6ac1cc58..cacfb3dbf 100644
--- a/agents/gsd-user-profiler.md
+++ b/agents/gsd-user-profiler.md
@@ -38,7 +38,7 @@ Key characteristics of the input:
 </input>
 
 <reference>
-@get-shit-done/references/user-profiling.md
+@~/.claude/get-shit-done/references/user-profiling.md
 
 This is the detection heuristics rubric. Read it in full before analyzing any messages. It defines:
 - The 8 dimensions and their rating spectrums
@@ -52,7 +52,7 @@ This is the detection heuristics rubric. Read it in full before analyzing any me
 <process>
 
 <step name="load_rubric">
-Read the user-profiling reference document at `get-shit-done/references/user-profiling.md` to load:
+Read the user-profiling reference document at `~/.claude/get-shit-done/references/user-profiling.md` to load:
 - All 8 dimension definitions with rating spectrums
 - Signal patterns and detection heuristics per dimension
 - Confidence scoring thresholds (HIGH: 10+ signals across 2+ projects, MEDIUM: 5-9, LOW: <5, UNSCORED: 0)
diff --git a/commands/gsd/cleanup.md b/commands/gsd/cleanup.md
index c95b2af1b..874bdeab2 100644
--- a/commands/gsd/cleanup.md
+++ b/commands/gsd/cleanup.md
@@ -1,6 +1,11 @@
 ---
 name: gsd:cleanup
 description: Archive accumulated phase directories from completed milestones
+allowed-tools:
+  - Read
+  - Write
+  - Bash
+  - AskUserQuestion
 ---
 <objective>
 Archive phase directories from completed milestones into `.planning/milestones/v{X.Y}-phases/`.
diff --git a/commands/gsd/help.md b/commands/gsd/help.md
index d4fedc277..212d24c1a 100644
--- a/commands/gsd/help.md
+++ b/commands/gsd/help.md
@@ -1,6 +1,8 @@
 ---
 name: gsd:help
 description: Show available GSD commands and usage guide
+allowed-tools:
+  - Read
 ---
 <objective>
 Display the complete GSD command reference.
diff --git a/commands/gsd/join-discord.md b/commands/gsd/join-discord.md
index 06c218a4e..4290e709f 100644
--- a/commands/gsd/join-discord.md
+++ b/commands/gsd/join-discord.md
@@ -1,6 +1,7 @@
 ---
 name: gsd:join-discord
 description: Join the GSD Discord community
+allowed-tools: []
 ---
 
 <objective>
diff --git a/commands/gsd/reapply-patches.md b/commands/gsd/reapply-patches.md
index 39bc93377..e9d0cfbd4 100644
--- a/commands/gsd/reapply-patches.md
+++ b/commands/gsd/reapply-patches.md
@@ -1,4 +1,5 @@
 ---
+name: gsd:reapply-patches
 description: Reapply local modifications after a GSD update
 allowed-tools: Read, Write, Edit, Bash, Glob, Grep, AskUserQuestion
 ---
@@ -223,22 +224,13 @@ Each matching commit represents an intentional user modification. Use the commit
 
 **Never report `Skipped — no custom content`.** If a file is in the backup, it has custom content.
 
-## Step 5: Update manifest
-
-After reapplying, regenerate the file manifest so future updates correctly detect these as user modifications:
-
-```bash
-# The manifest will be regenerated on next /gsd:update
-# For now, just note which files were modified
-```
-
-## Step 6: Cleanup option
+## Step 5: Cleanup option
 
 Ask user:
 - "Keep patch backups for reference?" → preserve `gsd-local-patches/`
 - "Clean up patch backups?" → remove `gsd-local-patches/` directory
 
-## Step 7: Report
+## Step 6: Report
 
 ```
 ## Patches Reapplied
diff --git a/commands/gsd/review-backlog.md b/commands/gsd/review-backlog.md
index 91de5dd83..7b34fec89 100644
--- a/commands/gsd/review-backlog.md
+++ b/commands/gsd/review-backlog.md
@@ -5,6 +5,7 @@ allowed-tools:
   - Read
   - Write
   - Bash
+  - AskUserQuestion
 ---
 
 <objective>
diff --git a/commands/gsd/workstreams.md b/commands/gsd/workstreams.md
index 7a6677e35..58c680fa2 100644
--- a/commands/gsd/workstreams.md
+++ b/commands/gsd/workstreams.md
@@ -1,5 +1,10 @@
 ---
+name: gsd:workstreams
 description: Manage parallel workstreams — list, create, switch, status, progress, complete, and resume
+allowed-tools:
+  - Read
+  - Write
+  - Bash
 ---
 
 # /gsd:workstreams