Document .ignore negation rule for fs tools

.ignore

@@ -20,7 +20,9 @@
 !.github/**
 !justfile
 
-# Then the exclusions (applied within the un-ignored trees)
+# Then the exclusions (applied within the un-ignored trees).
+# Re-including a subtree of an excluded dir needs BOTH lines:
+# !/path/dir/ and !/path/dir/**
 .jp/conversations/
 .jp/local-conversations/
 docs/.yarn/

.jp/mcp/tools/fs/grep_files.toml

@@ -14,6 +14,11 @@ If the number of results exceeds 100, the `context` option is disabled, and 50
 matches are returned without context. You can re-run the tool with a more
 specific pattern or limited to specific paths to narrow down the results with
 context.
+
+Searches honor the workspace `.ignore` file with gitignore semantics,
+including negations. Files inside an excluded tree stay hidden unless the
+directory and its contents are negated separately and seemingly redundantly
+(`!/target/doc/` and `!/target/doc/**`).
 """
 
 examples = """

.jp/mcp/tools/fs/list_files.toml

@@ -5,6 +5,14 @@ run = "unattended"
 source = "local"
 command = "just serve-tools {{context}} {{tool}}"
 summary = "List files in the project's local filesystem."
+description = """
+Results honor the workspace `.ignore` file with gitignore semantics,
+including negations. Note the gitignore re-inclusion rule: files inside
+an excluded tree stay hidden unless the directory and its contents are
+negated separately and seemingly redundantly (`!/target/doc/` and
+`!/target/doc/**`). If a file exists on disk but is absent from the
+listing, it matched an `.ignore` rule.
+"""
 
 examples = """
 List all Rust files: