diff --git a/docs/src/content/docs/guides/compilation.md b/docs/src/content/docs/guides/compilation.md
index 23de213b..3d89ab31 100644
--- a/docs/src/content/docs/guides/compilation.md
+++ b/docs/src/content/docs/guides/compilation.md
@@ -234,6 +234,8 @@ Optimizing instruction placement...
 Generated 4 AGENTS.md files with guaranteed coverage
 ```
 
+> **[!] Missing `applyTo`:** If any instruction file is missing a valid `applyTo` frontmatter field, `apm compile` emits a warning for each affected file across all compilation modes. Instructions without `applyTo` are treated as global (matching all files) which can inflate context load. Add a glob pattern to each `.instructions.md` frontmatter to silence the warning and improve optimization accuracy.
+
 ### Mathematical Analysis Mode
 
 ```bash
@@ -287,7 +289,7 @@ compilation:
 
 #### Directory Exclusion Patterns
 
-Use the `exclude` field to skip directories during compilation, improving performance in large monorepos:
+Use the `exclude` field to skip directories during both primitive discovery and compilation. Excluded paths are filtered before any scanning begins, so matched files never appear in compiled output even if they would otherwise match an instruction pattern. This improves performance in large monorepos and prevents duplicate instructions from leaking through:
 
 **Pattern Syntax:**
 - `tmp` - Matches directory named "tmp" at any depth
diff --git a/docs/src/content/docs/guides/marketplaces.md b/docs/src/content/docs/guides/marketplaces.md
index b969022c..17cef84d 100644
--- a/docs/src/content/docs/guides/marketplaces.md
+++ b/docs/src/content/docs/guides/marketplaces.md
@@ -80,6 +80,13 @@ This registers the marketplace and fetches its `marketplace.json`. By default AP
 apm marketplace add acme/plugin-marketplace --name acme-plugins --branch release
 ```
 
+**GitHub Enterprise Server:** If `GITHUB_HOST` is set, `apm marketplace add` resolves bare `owner/repo` references against your GHES instance, the same way `apm install` does. Set the variable before running the command:
+
+```bash
+export GITHUB_HOST=github.company.com
+apm marketplace add internal-org/plugin-marketplace
+```
+
 ## List registered marketplaces
 
 ```bash
diff --git a/docs/src/content/docs/guides/skills.md b/docs/src/content/docs/guides/skills.md
index 9cdb59ec..ca3df3de 100644
--- a/docs/src/content/docs/guides/skills.md
+++ b/docs/src/content/docs/guides/skills.md
@@ -376,6 +376,17 @@ If you see a skill name validation warning:
 1. **Check naming:** Names must be lowercase, 1-64 chars, hyphens only (no underscores)
 2. **Auto-normalization:** APM automatically normalizes invalid names when possible
 
+### Native Skill Name Collision
+
+If two installed packages deploy a native skill with the same name, APM emits a warning during install:
+
+```
+[!] Native skill name collision: "code-review" is deployed by both acme/code-review and corp/standards.
+    The last package installed wins. Rename one skill or remove the conflicting package.
+```
+
+To resolve: either rename the `SKILL.md` file in one of the packages, or remove the package that is shadowing the other. The last package installed takes precedence at the filesystem level.
+
 ### Metadata Missing
 
 If skill lacks APM metadata: