Making sense of npm dependencies

I'm trying to figure out exactly what's going on with npm dependencies.

The shortest specific form of my question is: given that my transitive dependency graph invokes a certain package multiple times with different versions, why are those different versions not showing up in either npm list or the file system?

I don't want to clutter the global namespace with junk just for testing, so will use my actual current project; it's small enough to be clear, I think.

C:\ayane>npm list
ayane@3.0.1 C:\ayane
+-- clause-normal-form@2.4.0
| +-- big-integer@1.6.22
| +-- big-rational@0.10.6
| +-- clone@2.1.1
| `-- lodash@4.17.4
+-- command-files@1.1.0
| `-- glob@7.1.1
|   +-- fs.realpath@1.0.0
|   +-- inflight@1.0.6
|   | `-- wrappy@1.0.2
|   +-- inherits@2.0.3
|   +-- minimatch@3.0.3
|   | `-- brace-expansion@1.1.7
|   |   +-- balanced-match@0.4.2
|   |   `-- concat-map@0.0.1
|   +-- once@1.4.0
|   `-- path-is-absolute@1.0.1
+-- commander@2.9.0
| `-- graceful-readlink@1.0.1
+-- dimacs-parser@2.3.0
+-- get-stdin@5.0.1
+-- iop@1.4.1
`-- tptp-parser@2.5.1

That looks fine so far except ayane depends on clause-normal-form 2.4.0 but dimacs-parser and tptp-parser depend on clause-normal-form 2.3.0; why is this not showing in the above?

C:\ayane>tree /a
Folder PATH listing for volume OS
Volume serial number is C685-B1F1
C:.
\---node_modules
    +---.bin
    +---balanced-match
    +---big-integer
    +---big-rational
    +---brace-expansion
    +---clause-normal-form
    +---clone
    +---command-files
    +---commander
    +---concat-map
    |   +---example
    |   \---test
    +---dimacs-parser
    +---fs.realpath
    +---get-stdin
    +---glob
    +---graceful-readlink
    +---inflight
    +---inherits
    +---iop
    +---lodash
    |   \---fp
    +---minimatch
    +---once
    +---path-is-absolute
    +---tptp-parser
    \---wrappy

Same question: why is only one clause-normal-form directory appearing?

via rwallace