Fix four SPKGs with irregular directory structures

Imported from <a href="http://trac.sagemath.org/sage_trac/ticket/12694">trac #12694</a>.

The following SPKGs do not have a `src/` directory:

```
sage_scripts
extcode
libm4ri
sage_root
elliptic_curves
graphs
sage
polytopes_db
```
The sage spkgs are obviously supposed to be irregular (I guess) but the other four - `libm4ri`, `elliptic_curves`, `graphs`, and `polytopes_db` should follow the guidelines given in the developers' guide and have a `src/` directory.

----
Install:

 * http://boxen.math.washington.edu/home/keshav/files/fixed-spkgs/elliptic_curves-0.5.spkg
 * http://boxen.math.washington.edu/home/keshav/files/fixed-spkgs/libm4ri-20111004.p1.spkg
 * http://boxen.math.washington.edu/home/keshav/files/fixed-spkgs/graphs-20070722.p2.spkg
 * http://boxen.math.washington.edu/home/keshav/files/fixed-spkgs/polytopes_db-20100210.p1.spkg

Reported by: kini

Component: packages

CC: rohana,, malb,, ekirkman,, novoselt,, jason,, was

Report Upstream: N/A

Authors: Keshav Kini

Dependencies: <a href="http://trac.sagemath.org/sage_trac/ticket/12644">trac #12644</a>

Work issues: 

Reviewers: R. Andrew Ohana

Merged in: sage-5.0.beta10

Attachments: <ol></ol>